Author: tlinnet
Date: Wed May 28 19:17:27 2014
New Revision: 23567
URL: http://svn.gna.org/viewcvs/relax?rev=23567&view=rev
Log:
Converting back to having back_calc as a function argument to model IT99:
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/it99.py
branches/disp_speed/target_functions/relax_disp.py
branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py
Modified: branches/disp_speed/lib/dispersion/it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/lib/dispersion/it99.py?rev=23567&r1=23566&r2=23567&view=diff
==============================================================================
--- branches/disp_speed/lib/dispersion/it99.py (original)
+++ branches/disp_speed/lib/dispersion/it99.py Wed May 28 19:17:27 2014
@@ -76,7 +76,7 @@
from numpy import array, isfinite, sqrt, sum
-def r2eff_IT99(r20=None, pA=None, pB=None, dw=None, tex=None,
cpmg_frqs=None, num_points=None):
+def r2eff_IT99(r20=None, pA=None, pB=None, dw=None, tex=None,
cpmg_frqs=None, back_calc=None, num_points=None):
"""Calculate the R2eff values for the IT99 model.
See the module docstring for details.
@@ -94,7 +94,10 @@
@type tex: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
@type cpmg_frqs: numpy rank-1 float array
- @keyword num_points: The number of points on the dispersion curve,
equal to the length of the cpmg_frqs.
+ @type tcp: numpy rank-1 float array
+ @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
"""
@@ -110,7 +113,8 @@
# Catch zeros (to avoid pointless mathematical operations).
# This will result in no exchange, returning flat lines.
if numer == 0.0:
- return array([r20]*num_points)
+ back_calc[:] = array([r20]*num_points)
+ return
# The effective rotating frame field.
omega_1eff4 = 2304.0 * cpmg_frqs**4
@@ -127,4 +131,4 @@
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=23567&r1=23566&r2=23567&view=diff
==============================================================================
--- branches/disp_speed/target_functions/relax_disp.py (original)
+++ branches/disp_speed/target_functions/relax_disp.py Wed May 28 19:17:27
2014
@@ -1015,7 +1015,7 @@
dw_frq = dw[si] * self.frqs[0][si][mi]
# Back calculate the R2eff values.
- self.back_calc[0][si][mi][0] =
r2eff_IT99(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq, tex=tex,
cpmg_frqs=self.cpmg_frqs[0][mi][0],
num_points=self.num_disp_points[0][si][mi][0])
+ r2eff_IT99(r20=R20[r20_index], pA=pA, pB=pB, dw=dw_frq,
tex=tex, cpmg_frqs=self.cpmg_frqs[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_it99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_speed/test_suite/unit_tests/_lib/_dispersion/test_it99.py?rev=23567&r1=23566&r2=23567&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
Wed May 28 19:17:27 2014
@@ -44,6 +44,7 @@
self.ncyc = array([2, 4, 8, 10, 20, 40, 500])
relax_times = 0.04
self.cpmg_frqs = self.ncyc / relax_times
+ self.R2eff = zeros(self.num_points, float64)
# The spin Larmor frequencies.
self.sfrq = 200. * 1E6
@@ -56,15 +57,15 @@
pB, dw_frq, tex = self.param_conversion(pA=self.pA, kex=self.kex,
dw=self.dw, sfrq=self.sfrq)
# Calculate the R2eff values.
- R2eff = r2eff_IT99(r20=self.r20, pA=self.pA, pB=pB, dw=dw_frq,
tex=tex, cpmg_frqs=self.cpmg_frqs, num_points=self.num_points)
+ r2eff_IT99(r20=self.r20, pA=self.pA, pB=pB, dw=dw_frq, tex=tex,
cpmg_frqs=self.cpmg_frqs, back_calc=self.R2eff, num_points=self.num_points)
# Check all R2eff values.
if self.kex > 1.e5:
for i in range(self.num_points):
- self.assertAlmostEqual(R2eff[i], self.r20, 2)
+ self.assertAlmostEqual(self.R2eff[i], self.r20, 2)
else:
for i in range(self.num_points):
- self.assertAlmostEqual(R2eff[i], self.r20)
+ self.assertAlmostEqual(self.R2eff[i], self.r20)
def param_conversion(self, pA=None, kex=None, dw=None, sfrq=None):
r23567 - in /branches/disp_speed: lib/dispersion/ target_functions/ test_suite/unit_tests/_lib/_dispersion/