Author: tlinnet
Date: Wed Jun 11 19:37:40 2014
New Revision: 23849
URL: http://svn.gna.org/viewcvs/relax?rev=23849&view=rev
Log:
Modified model B14 lib file to faster numpy multidimensional mode.
The implementations comes almost directly from the CR72 model file.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/lib/dispersion/b14.py
Modified: branches/disp_spin_speed/lib/dispersion/b14.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/b14.py?rev=23849&r1=23848&r2=23849&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/b14.py (original)
+++ branches/disp_spin_speed/lib/dispersion/b14.py Wed Jun 11 19:37:40
2014
@@ -110,7 +110,8 @@
"""
# Python module imports.
-from numpy import arccosh, arctan2, array, cos, cosh, isfinite, log, max,
power, sin, sinh, sqrt, sum
+from numpy import arccosh, arctan2, array, cos, cosh, fabs, isfinite, log,
max, min, power, sin, sinh, sqrt, sum
+from numpy.ma import fix_invalid, masked_greater_equal, masked_where
# Repetitive calculations (to speed up calculations).
g_fact = 1/sqrt(2)
@@ -122,15 +123,15 @@
@keyword r20a: The R20 parameter value of state A (R2 with no
exchange).
- @type r20a: float
+ @type r20a: numpy float array of rank [NE][NS][[NM][NO][ND]
@keyword r20b: The R20 parameter value of state B (R2 with no
exchange).
- @type r20b: float
+ @type r20b: numpy float array of rank [NE][NS][[NM][NO][ND]
@keyword pA: The population of state A.
@type pA: float
@keyword pB: The population of state B.
@type pB: float
@keyword dw: The chemical exchange difference between states
A and B in rad/s.
- @type dw: float
+ @type dw: numpy float array of rank [NE][NS][[NM][NO][ND]
@keyword kex: The kex parameter value (the exchange rate in
rad/s).
@type kex: float
@keyword k_AB: The rate of exchange from site A to B (rad/s).
@@ -138,21 +139,31 @@
@keyword k_BA: The rate of exchange from site B to A (rad/s).
@type k_BA: float
@keyword ncyc: The matrix exponential power array. The number
of CPMG blocks.
- @type ncyc: numpy int16, rank-1 array
+ @type ncyc: numpy int16 array of rank [NE][NS][[NM][NO][ND]
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
- @type inv_tcpmg: float
+ @type inv_tcpmg: numpy float array of rank [NE][NS][[NM][NO][ND]
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
- @type tcp: numpy rank-1 float array
+ @type tcp: numpy float array of rank [NE][NS][[NM][NO][ND]
@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
+ @type back_calc: numpy float array of rank [NE][NS][[NM][NO][ND]
@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
"""
+ # Flag to tell if values should be replaced if max_e_zero in cosh
function is violated.
+ t_dw_zero = False
+ t_max_e_zero = False
+
# 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:
- back_calc[:] = array([r20a]*num_points)
- return
+ # Test if pA or kex is zero.
+ if kex == 0.0 or pA == 1.0:
+ back_calc[:] = r20a
+ return
+
+ # Test if dw is zero. Wait for replacement, since this is spin specific.
+ if min(fabs(dw)) == 0.0:
+ t_dw_zero = True
+ mask_dw_zero = masked_where(dw == 0.0, dw)
# Repetitive calculations (to speed up calculations).
deltaR2 = r20a - r20b
@@ -203,8 +214,10 @@
# Catch math domain error of sinh(val > 710).
# This is when E0 > 710.
if max(E0) > 700:
- back_calc[:] = array([r20a]*num_points)
- return
+ t_max_e_zero = True
+ mask_max_e_zero = masked_greater_equal(E0, 700.0)
+ # To prevent math errors, set e_zero to 1.
+ E0[mask_max_e_zero.mask] = 1.0
# Derived from chemical shifts #E2 = complex(0,-2.0 * tcp * (F00I -
f11I)).
E2 = two_tcp * g4
@@ -245,11 +258,19 @@
# R2eff = R2eff_CR72 - inv_tcpmg * log(Tog.real)
# Fastest calculation.
- R2eff = (r20a + r20b + kex) / 2.0 - inv_tcpmg * ( ncyc *
arccosh(v1c.real) + log(Tog.real) )
+ back_calc[:] = (r20a + r20b + kex) / 2.0 - inv_tcpmg * ( ncyc *
arccosh(v1c.real) + log(Tog.real) )
+
+ # Replace data in array.
+ # If dw is zero.
+ if t_dw_zero:
+ back_calc[mask_dw_zero.mask] = r20a[mask_dw_zero.mask]
+
+ # If eta_pos above 700.
+ if t_max_e_zero:
+ back_calc[mask_max_e_zero.mask] = r20a[mask_max_e_zero.mask]
# 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(R2eff)):
- R2eff = array([1e100]*num_points)
-
- back_calc[:] = R2eff
+ if not isfinite(sum(back_calc)):
+ # Replaces nan, inf, etc. with fill value.
+ fix_invalid(back_calc, copy=False, fill_value=1e100)
r23849 - /branches/disp_spin_speed/lib/dispersion/b14.py