Author: bugman
Date: Fri Jul 19 20:25:03 2013
New Revision: 20425
URL: http://svn.gna.org/viewcvs/relax?rev=20425&view=rev
Log:
Speed ups for the 'LM63 3-site' target function.
Some mathematical operations have been shifted from the library code into the
target function so
that is only calculates once per function call.
Modified:
branches/relax_disp/lib/dispersion/lm63_3site.py
branches/relax_disp/target_functions/relax_disp.py
Modified: branches/relax_disp/lib/dispersion/lm63_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/lib/dispersion/lm63_3site.py?rev=20425&r1=20424&r2=20425&view=diff
==============================================================================
--- branches/relax_disp/lib/dispersion/lm63_3site.py (original)
+++ branches/relax_disp/lib/dispersion/lm63_3site.py Fri Jul 19 20:25:03 2013
@@ -48,7 +48,7 @@
from math import tanh
-def r2eff_LM63_3site(r20=None, phi_ex_B=None, phi_ex_C=None, kB=None,
kC=None, cpmg_frqs=None, back_calc=None, num_points=None):
+def r2eff_LM63_3site(r20=None, rex_B=None, rex_C=None, quart_kB=None,
quart_kC=None, cpmg_frqs=None, back_calc=None, num_points=None):
"""Calculate the R2eff values for the LM63 3-site model.
See the module docstring for details.
@@ -56,14 +56,14 @@
@keyword r20: The R20 parameter value (R2 with no exchange).
@type r20: float
- @keyword phi_ex_B: The phi_ex_B parameter value.
- @type phi_ex_B: float
- @keyword phi_ex_C: The phi_ex_C parameter value.
- @type phi_ex_C: float
- @keyword kB: Approximate chemical exchange rate constant
between sites A and B (the exchange rate in rad/s).
- @type kB: float
- @keyword kC: Approximate chemical exchange rate constant
between sites A and C (the exchange rate in rad/s).
- @type kC: float
+ @keyword rex_B: The phi_ex_B / kB parameter value.
+ @type rex_B: float
+ @keyword rex_C: The phi_ex_C / kC parameter value.
+ @type rex_C: float
+ @keyword quart_kB: Approximate chemical exchange rate constant
between sites A and B (the exchange rate in rad/s) divided by 4.
+ @type quart_kB: float
+ @keyword quart_kC: Approximate chemical exchange rate constant
between sites A and C (the exchange rate in rad/s) divided by 4.
+ @type quart_kC: float
@keyword cpmg_frqs: The CPMG nu1 frequencies.
@type cpmg_frqs: 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.
@@ -72,24 +72,18 @@
@type num_points: int
"""
- # Repetitive calculations (to speed up calculations).
- rex_B = phi_ex_B / kB
- rex_C = phi_ex_C / kC
- kB_4 = 4.0 / kB
- kC_4 = 4.0 / kC
-
# Loop over the time points, back calculating the R2eff values.
for i in range(num_points):
# Catch zeros.
- if phi_ex_B == 0.0 and phi_ex_C == 0.0:
+ if rex_B == 0.0 and rex_C == 0.0:
back_calc[i] = r20
# Avoid divide by zero.
- elif kB == 0.0 or kC == 0.0:
+ elif quart_kB == 0.0 or quart_kC == 0.0:
back_calc[i] = 1e100
# The full formula.
else:
back_calc[i] = r20
- back_calc[i] += rex_B * (1.0 - kB_4 * cpmg_frqs[i] * tanh(kB /
(4.0 * cpmg_frqs[i])))
- back_calc[i] += rex_C * (1.0 - kC_4 * cpmg_frqs[i] * tanh(kC /
(4.0 * cpmg_frqs[i])))
+ back_calc[i] += rex_B * (1.0 - cpmg_frqs[i] * tanh(quart_kB *
cpmg_frqs[i]) / quart_kB)
+ back_calc[i] += rex_C * (1.0 - cpmg_frqs[i] * tanh(quart_kC *
cpmg_frqs[i]) / quart_kC)
Modified: branches/relax_disp/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/target_functions/relax_disp.py?rev=20425&r1=20424&r2=20425&view=diff
==============================================================================
--- branches/relax_disp/target_functions/relax_disp.py (original)
+++ branches/relax_disp/target_functions/relax_disp.py Fri Jul 19 20:25:03
2013
@@ -538,6 +538,12 @@
kB = params[self.end_index[2]]
kC = params[self.end_index[2]+1]
+ # Once off parameter conversions.
+ rex_B = phi_ex_B / kB
+ rex_C = phi_ex_C / kC
+ quart_kB = kB / 4.0
+ quart_kC = kC / 4.0
+
# Initialise.
chi2_sum = 0.0
@@ -548,13 +554,13 @@
# The R20 index.
r20_index = frq_index + spin_index*self.num_frq
- # Convert phi_ex from ppm^2 to (rad/s)^2.
+ # Convert phi_ex (or rex) from ppm^2 to (rad/s)^2.
frq2 = self.frqs[spin_index, frq_index]**2
- phi_ex_B_scaled = phi_ex_B[spin_index] * frq2
- phi_ex_C_scaled = phi_ex_C[spin_index] * frq2
+ rex_B_scaled = rex_B[spin_index] * frq2
+ rex_C_scaled = rex_C[spin_index] * frq2
# Back calculate the R2eff values.
- r2eff_LM63_3site(r20=R20[r20_index],
phi_ex_B=phi_ex_B_scaled, phi_ex_C=phi_ex_C_scaled, kB=kB, kC=kC,
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points)
+ r2eff_LM63_3site(r20=R20[r20_index], rex_B=rex_B_scaled,
rex_C=rex_C_scaled, quart_kB=quart_kB, quart_kC=quart_kC,
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc[spin_index, frq_index],
num_points=self.num_disp_points)
# 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 point_index in range(self.num_disp_points):
r20425 - in /branches/relax_disp: lib/dispersion/lm63_3site.py target_functions/relax_disp.py