Author: tlinnet
Date: Fri Jun 20 15:48:35 2014
New Revision: 24207
URL: http://svn.gna.org/viewcvs/relax?rev=24207&view=rev
Log:
Moved the Bloch-McConnell matrix for 3-site exchange, into the
lib/dispersion/ns_matrices.py.
This is to standard the code.
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_matrices.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_matrices.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_matrices.py?rev=24207&r1=24206&r2=24207&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_matrices.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_matrices.py Fri Jun 20
15:48:35 2014
@@ -511,6 +511,51 @@
matrix = (m_r20a_tcp + m_r20b_tcp + m_k_AB_tcp + m_k_BA_tcp + m_dw_tcp_C)
return matrix
+
+
+def rmmq_3site(matrix=None, R20A=None, R20B=None, R20C=None, dw_AB=None,
dw_AC=None, k_AB=None, k_BA=None, k_BC=None, k_CB=None, k_AC=None, k_CA=None):
+ """The Bloch-McConnell matrix for 3-site exchange.
+
+ @keyword matrix: The matrix to populate.
+ @type matrix: numpy rank-2, 3D complex64 array
+ @keyword R20A: The transverse, spin-spin relaxation rate for
state A.
+ @type R20A: numpy float array of rank [NS][NM][NO][ND]
+ @keyword R20B: The transverse, spin-spin relaxation rate for
state B.
+ @type R20B: numpy float array of rank [NS][NM][NO][ND]
+ @keyword R20C: The transverse, spin-spin relaxation rate for
state C.
+ @type R20C: numpy float array of rank [NS][NM][NO][ND]
+ @keyword dw_AB: The combined chemical exchange difference
parameters between states A and B in rad/s. This can be any combination of
dw and dwH.
+ @type dw_AB: numpy float array of rank [NS][NM][NO][ND]
+ @keyword dw_AC: The combined chemical exchange difference
parameters between states A and C in rad/s. This can be any combination of
dw and dwH.
+ @type dw_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
+ """
+
+ # The first row.
+ matrix[0, 0] = -k_AB - k_AC - R20A
+ matrix[0, 1] = k_BA
+ matrix[0, 2] = k_CA
+
+ # The second row.
+ matrix[1, 0] = k_AB
+ matrix[1, 1] = -k_BA - k_BC + 1.j*dw_AB - R20B
+ matrix[1, 2] = k_CB
+
+ # The third row.
+ matrix[2, 0] = k_AC
+ matrix[2, 1] = k_BC
+ matrix[2, 2] = -k_CB - k_CA + 1.j*dw_AC - R20C
def rr1rho_3d_3site(matrix=None, R1=None, r1rho_prime=None, pA=None,
pB=None, pC=None, wA=None, wB=None, wC=None, w1=None, k_AB=None, k_BA=None,
k_BC=None, k_CB=None, k_AC=None, k_CA=None):
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=24207&r1=24206&r2=24207&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Fri Jun 20
15:48:35 2014
@@ -61,53 +61,9 @@
# relax module imports.
from lib.float import isNaN
+from lib.dispersion.ns_matrices import rmmq_3site
from lib.linear_algebra.matrix_exponential import matrix_exponential
from lib.linear_algebra.matrix_power import square_matrix_power
-
-
-def populate_matrix(matrix=None, R20A=None, R20B=None, R20C=None,
dw_AB=None, dw_AC=None, k_AB=None, k_BA=None, k_BC=None, k_CB=None,
k_AC=None, k_CA=None):
- """The Bloch-McConnell matrix for 3-site exchange.
-
- @keyword matrix: The matrix to populate.
- @type matrix: numpy rank-2, 3D complex64 array
- @keyword R20A: The transverse, spin-spin relaxation rate for
state A.
- @type R20A: numpy float array of rank [NS][NM][NO][ND]
- @keyword R20B: The transverse, spin-spin relaxation rate for
state B.
- @type R20B: numpy float array of rank [NS][NM][NO][ND]
- @keyword R20C: The transverse, spin-spin relaxation rate for
state C.
- @type R20C: numpy float array of rank [NS][NM][NO][ND]
- @keyword dw_AB: The combined chemical exchange difference
parameters between states A and B in rad/s. This can be any combination of
dw and dwH.
- @type dw_AB: numpy float array of rank [NS][NM][NO][ND]
- @keyword dw_AC: The combined chemical exchange difference
parameters between states A and C in rad/s. This can be any combination of
dw and dwH.
- @type dw_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
- """
-
- # The first row.
- matrix[0, 0] = -k_AB - k_AC - R20A
- matrix[0, 1] = k_BA
- matrix[0, 2] = k_CA
-
- # The second row.
- matrix[1, 0] = k_AB
- matrix[1, 1] = -k_BA - k_BC + 1.j*dw_AB - R20B
- matrix[1, 2] = k_CB
-
- # The third row.
- matrix[2, 0] = k_AC
- matrix[2, 1] = k_BC
- 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,
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):
@@ -206,8 +162,8 @@
num_points_i = num_points[si, mi, oi]
# Populate the m1 and m2 matrices (only once per function
call for speed).
- populate_matrix(matrix=m1, R20A=r20a_i, R20B=r20b_i,
R20C=r20c_i, dw_AB=-dw_AB_i - dwH_AB_i, dw_AC=-dw_AC_i - dwH_AC_i, k_AB=k_AB,
k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA) # D+ matrix
component.
- populate_matrix(matrix=m2, R20A=r20a_i, R20B=r20b_i,
R20C=r20c_i, dw_AB=dw_AB_i - dwH_AB_i, dw_AC=dw_AC_i - dwH_AC_i, k_AB=k_AB,
k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA) # Z- matrix
component.
+ rmmq_3site(matrix=m1, R20A=r20a_i, R20B=r20b_i, R20C=r20c_i,
dw_AB=-dw_AB_i - dwH_AB_i, dw_AC=-dw_AC_i - dwH_AC_i, k_AB=k_AB, k_BA=k_BA,
k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA) # D+ matrix component.
+ rmmq_3site(matrix=m2, R20A=r20a_i, R20B=r20b_i, R20C=r20c_i,
dw_AB=dw_AB_i - dwH_AB_i, dw_AC=dw_AC_i - dwH_AC_i, k_AB=k_AB, k_BA=k_BA,
k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA) # Z- matrix component.
# Loop over the time points, back calculating the R2eff
values.
for i in range(num_points_i):
@@ -384,8 +340,8 @@
num_points_i = num_points[si, mi, oi]
# Populate the m1 and m2 matrices (only once per function
call for speed).
- populate_matrix(matrix=m1, R20A=r20a_i, R20B=r20b_i,
R20C=r20c_i, dw_AB=dw_AB_i, dw_AC=dw_AC_i, k_AB=k_AB, k_BA=k_BA, k_BC=k_BC,
k_CB=k_CB, k_AC=k_AC, k_CA=k_CA)
- populate_matrix(matrix=m2, R20A=r20a_i, R20B=r20b_i,
R20C=r20c_i, dw_AB=-dw_AB_i, dw_AC=-dw_AC_i, k_AB=k_AB, k_BA=k_BA, k_BC=k_BC,
k_CB=k_CB, k_AC=k_AC, k_CA=k_CA)
+ rmmq_3site(matrix=m1, R20A=r20a_i, R20B=r20b_i, R20C=r20c_i,
dw_AB=dw_AB_i, dw_AC=dw_AC_i, k_AB=k_AB, k_BA=k_BA, k_BC=k_BC, k_CB=k_CB,
k_AC=k_AC, k_CA=k_CA)
+ rmmq_3site(matrix=m2, R20A=r20a_i, R20B=r20b_i, R20C=r20c_i,
dw_AB=-dw_AB_i, dw_AC=-dw_AC_i, k_AB=k_AB, k_BA=k_BA, k_BC=k_BC, k_CB=k_CB,
k_AC=k_AC, k_CA=k_CA)
# Loop over the time points, back calculating the R2eff
values.
for i in range(num_points_i):
r24207 - in /branches/disp_spin_speed/lib/dispersion: ns_matrices.py ns_mmq_3site.py