Author: tlinnet
Date: Wed Jun 18 18:52:37 2014
New Revision: 24119
URL: http://svn.gna.org/viewcvs/relax?rev=24119&view=rev
Log:
Moved the parameter conversion for ns mmq 3site into lib function.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion
models for Clustered analysis.
Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
branches/disp_spin_speed/target_functions/relax_disp.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=24119&r1=24118&r2=24119&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Wed Jun 18
18:52:37 2014
@@ -110,7 +110,7 @@
matrix[2, 2] = -k_CB - k_CA + 1.j*dw_AC - R20C
-def r2eff_ns_mmq_3site_mq(M0=None, F_vector=array([1, 0, 0], float64),
m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, pB=None, pC=None,
dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, k_AB=None, k_BA=None,
k_BC=None, k_CB=None, k_AC=None, k_CA=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
+def r2eff_ns_mmq_3site_mq(M0=None, F_vector=array([1, 0, 0], float64),
m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, pB=None,
dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, kex_AB=None, kex_BC=None,
kex_AC=None, inv_tcpmg=None, tcp=None, back_calc=None, num_points=None,
power=None):
"""The 3-site numerical solution to the Bloch-McConnell equation for MQ
data.
The notation used here comes from:
@@ -142,8 +142,6 @@
@type pA: float
@keyword pB: The population of state B.
@type pB: float
- @keyword pC: The population of state C.
- @type pC: float
@keyword dw_AB: The chemical exchange difference between states
A and B in rad/s.
@type dw_AB: numpy float array of rank [NS][NM][NO][ND]
@keyword dw_AC: The chemical exchange difference between states
A and C in rad/s.
@@ -152,18 +150,12 @@
@type dwH_AB: numpy float array of rank [NS][NM][NO][ND]
@keyword dwH_AC: The proton chemical exchange difference between
states A and C in rad/s.
@type dwH_AC: numpy float array of rank [NS][NM][NO][ND]
- @keyword k_AB: The rate of exchange from site A to B (rad/s).
- @type k_AB: float
- @keyword k_BA: The rate of exchange from site B to A (rad/s).
- @type k_BA: float
- @keyword k_BC: The rate of exchange from site B to C (rad/s).
- @type k_BC: float
- @keyword k_CB: The rate of exchange from site C to B (rad/s).
- @type k_CB: float
- @keyword k_AC: The rate of exchange from site A to C (rad/s).
- @type k_AC: float
- @keyword k_CA: The rate of exchange from site C to A (rad/s).
- @type k_CA: float
+ @keyword kex_AB: The exchange rate between sites A and B for
3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)
+ @type kex_AB: float
+ @keyword kex_BC: The exchange rate between sites A and C for
3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)
+ @type kex_BC: float
+ @keyword kex_AC: The exchange rate between sites B and C for
3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1)
+ @type kex_AC: float
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
@type inv_tcpmg: float
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@@ -176,6 +168,23 @@
@type power: numpy int array of rank [NS][NM][NO][ND]
"""
+ # Once off parameter conversions.
+ pC = 1.0 - pA - pB
+ pA_pB = pA + pB
+ pA_pC = pA + pC
+ pB_pC = pB + pC
+ k_BA = pA * kex_AB / pA_pB
+ k_AB = pB * kex_AB / pA_pB
+ k_CB = pB * kex_BC / pB_pC
+ k_BC = pC * kex_BC / pB_pC
+ k_CA = pA * kex_AC / pA_pC
+ k_AC = pC * kex_AC / pA_pC
+
+ # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
+ M0[0] = pA
+ M0[1] = pB
+ M0[2] = pC
+
# Extract shape of experiment.
NS, NM, NO = num_points.shape
@@ -283,7 +292,7 @@
back_calc[si, mi, oi, i]= -inv_tcpmg[si, mi, oi, i]
* log(Mx / pA)
-def r2eff_ns_mmq_3site_sq_dq_zq(M0=None, F_vector=array([1, 0, 0], float64),
m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, pB=None, pC=None,
dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, k_AB=None, k_BA=None,
k_BC=None, k_CB=None, k_AC=None, k_CA=None, inv_tcpmg=None, tcp=None,
back_calc=None, num_points=None, power=None):
+def r2eff_ns_mmq_3site_sq_dq_zq(M0=None, F_vector=array([1, 0, 0], float64),
m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, pB=None,
dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, kex_AB=None, kex_BC=None,
kex_AC=None, inv_tcpmg=None, tcp=None, back_calc=None, num_points=None,
power=None):
"""The 3-site numerical solution to the Bloch-McConnell equation for SQ,
ZQ, and DQ data.
The notation used here comes from:
@@ -311,8 +320,6 @@
@type pA: float
@keyword pB: The population of state B.
@type pB: float
- @keyword pC: The population of state C.
- @type pC: float
@keyword dw_AB: The combined chemical exchange difference
between states A and B in rad/s. It should be set to dwH for 1H SQ data, dw
for heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
@type dw_AB: numpy float array of rank [NS][NM][NO][ND]
@keyword dw_AC: The combined chemical exchange difference
between states A and C in rad/s. It should be set to dwH for 1H SQ data, dw
for heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
@@ -321,10 +328,12 @@
@type dwH_AB: numpy float array of rank [NS][NM][NO][ND]
@keyword dwH_AC: Unused - this is simply to match the
r2eff_mmq_3site_mq() function arguments.
@type dwH_AC: numpy float array of rank [NS][NM][NO][ND]
- @keyword k_AB: The rate of exchange from site A to B (rad/s).
- @type k_AB: float
- @keyword k_BA: The rate of exchange from site B to A (rad/s).
- @type k_BA: float
+ @keyword kex_AB: The exchange rate between sites A and B for
3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)
+ @type kex_AB: float
+ @keyword kex_BC: The exchange rate between sites A and C for
3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)
+ @type kex_BC: float
+ @keyword kex_AC: The exchange rate between sites B and C for
3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1)
+ @type kex_AC: float
@keyword inv_tcpmg: The inverse of the total duration of the CPMG
element (in inverse seconds).
@type inv_tcpmg: numpy float array of rank [NS][NM][NO][ND]
@keyword tcp: The tau_CPMG times (1 / 4.nu1).
@@ -337,6 +346,23 @@
@type power: numpy int array of rank [NS][NM][NO][ND]
"""
+ # Once off parameter conversions.
+ pC = 1.0 - pA - pB
+ pA_pB = pA + pB
+ pA_pC = pA + pC
+ pB_pC = pB + pC
+ k_BA = pA * kex_AB / pA_pB
+ k_AB = pB * kex_AB / pA_pB
+ k_CB = pB * kex_BC / pB_pC
+ k_BC = pC * kex_BC / pB_pC
+ k_CA = pA * kex_AC / pA_pC
+ k_AC = pC * kex_AC / pA_pC
+
+ # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
+ M0[0] = pA
+ M0[1] = pB
+ M0[2] = pC
+
# Extract shape of experiment.
NS, NM, NO = num_points.shape
Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24119&r1=24118&r2=24119&view=diff
==============================================================================
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18
18:52:37 2014
@@ -677,23 +677,8 @@
"""
# Once off parameter conversions.
- pC = 1.0 - pA - pB
- pA_pB = pA + pB
- pA_pC = pA + pC
- pB_pC = pB + pC
- k_BA = pA * kex_AB / pA_pB
- k_AB = pB * kex_AB / pA_pB
- k_CB = pB * kex_BC / pB_pC
- k_BC = pC * kex_BC / pB_pC
- k_CA = pA * kex_AC / pA_pC
- k_AC = pC * kex_AC / pA_pC
dw_AC = dw_AB + dw_BC
dwH_AC = dwH_AB + dwH_BC
-
- # This is a vector that contains the initial magnetizations
corresponding to the A and B state transverse magnetizations.
- self.M0[0] = pA
- self.M0[1] = pB
- self.M0[2] = pC
# Convert dw from ppm to rad/s. Use the out argument, to pass
directly to structure.
multiply( multiply.outer( dw_AB.reshape(1, self.NS),
self.nm_no_nd_ones ), self.frqs, out=self.dw_AB_struct )
@@ -744,7 +729,7 @@
aliased_dwH_AC = dw_AC_frq
# Back calculate the R2eff values for each experiment type.
- self.r2eff_ns_mmq[ei](M0=self.M0, m1=self.m1, m2=self.m2,
R20A=r20a, R20B=r20b, R20C=r20c, pA=pA, pB=pB, pC=pC, dw_AB=aliased_dw_AB,
dw_AC=aliased_dw_AC, dwH_AB=aliased_dwH_AB, dwH_AC=aliased_dwH_AC, k_AB=k_AB,
k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA,
inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei],
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei],
power=self.power[ei])
+ self.r2eff_ns_mmq[ei](M0=self.M0, m1=self.m1, m2=self.m2,
R20A=r20a, R20B=r20b, R20C=r20c, pA=pA, pB=pB, dw_AB=aliased_dw_AB,
dw_AC=aliased_dw_AC, dwH_AB=aliased_dwH_AB, dwH_AC=aliased_dwH_AC,
kex_AB=kex_AB, kex_BC=kex_BC, kex_AC=kex_AC,
inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei],
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei],
power=self.power[ei])
# Clean the data for all values, which is left over at the end of
arrays.
self.back_calc = self.back_calc*self.disp_struct
r24119 - in /branches/disp_spin_speed: lib/dispersion/ns_mmq_3site.py target_functions/relax_disp.py