Author: tlinnet
Date: Fri Jun 20 15:22:21 2014
New Revision: 24205
URL: http://svn.gna.org/viewcvs/relax?rev=24205&view=rev
Log:
Moved the matrices for Bloch-McConnell from lib ns_mmq_2site, since they are
now defined in ns_matrices.py
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_2site.py
Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24205&r1=24204&r2=24205&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Fri Jun 20
15:22:21 2014
@@ -55,102 +55,9 @@
# relax module imports.
from lib.float import isNaN
+from lib.dispersion.ns_matrices import rmmq_2site_rankN
from lib.linear_algebra.matrix_exponential import matrix_exponential,
matrix_exponential_rankN
from lib.linear_algebra.matrix_power import square_matrix_power
-
-
-def populate_matrix(matrix=None, R20A=None, R20B=None, dw=None, k_AB=None,
k_BA=None):
- """The Bloch-McConnell matrix for 2-site exchange.
-
- @keyword matrix: The matrix to populate.
- @type matrix: numpy rank-2, 2D complex64 array
- @keyword R20A: The transverse, spin-spin relaxation rate for
state A.
- @type R20A: float
- @keyword R20B: The transverse, spin-spin relaxation rate for
state B.
- @type R20B: float
- @keyword dw: 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: float
- @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
- """
-
- # Fill in the elements.
- matrix[0, 0] = -k_AB - R20A
- matrix[0, 1] = k_BA
- matrix[1, 0] = k_AB
- matrix[1, 1] = -k_BA + 1.j*dw - R20B
-
-
-def populate_matrix_rankN(R20A=None, R20B=None, dw=None, k_AB=None,
k_BA=None, tcp=None):
- """The Bloch-McConnell matrix for 2-site exchange, for rank
[NE][NS][NM][NO][ND][2][2].
-
- @keyword R20A: The transverse, spin-spin relaxation rate for
state A.
- @type R20A: numpy float array of rank [NE][NS][NM][NO][ND]
- @keyword R20B: The transverse, spin-spin relaxation rate for
state B.
- @type R20B: numpy float array of rank [NE][NS][NM][NO][ND]
- @keyword dw: 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: numpy float array of rank [NE][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 tcp: The tau_CPMG times (1 / 4.nu1).
- @type tcp: numpy float array of rank [NE][NS][NM][NO][ND]
- @return: The relaxation matrix.
- @rtype: numpy float array of rank
[NE][NS][NM][NO][ND][2][2]
- """
-
- # Pre-multiply with tcp.
- r20a_tcp = R20A * tcp
- r20b_tcp = R20B * tcp
- k_AB_tcp = k_AB * tcp
- k_BA_tcp = k_BA * tcp
- # Complex dw.
- dw_tcp_C = dw * tcp * 1j
-
- # Fill in the elements.
- #matrix[0, 0] = -k_AB - R20A
- #matrix[0, 1] = k_BA
- #matrix[1, 0] = k_AB
- #matrix[1, 1] = -k_BA + 1.j*dw - R20B
-
- m_r20a = array([
- [-1.0, 0.0],
- [0.0, 0.0],])
-
- m_r20b = array([
- [0.0, 0.0],
- [0.0, -1.0],])
-
- m_k_AB = array([
- [-1.0, 0.0],
- [1.0, 0.0],])
-
- m_k_BA = array([
- [0.0, 1.0],
- [0.0, -1.0],])
-
- m_dw = array([
- [0.0, 0.0],
- [0.0, 1.0],])
-
- # Multiply and expand.
- m_r20a_tcp = multiply.outer( r20a_tcp, m_r20a )
- m_r20b_tcp = multiply.outer( r20b_tcp, m_r20b )
-
- # Multiply and expand.
- m_k_AB_tcp = multiply.outer( k_AB_tcp, m_k_AB )
- m_k_BA_tcp = multiply.outer( k_BA_tcp, m_k_BA )
-
- # Multiply and expand.
- m_dw_tcp_C = multiply.outer( dw_tcp_C, m_dw )
-
- # Collect matrix.
- matrix = (m_r20a_tcp + m_r20b_tcp + m_k_AB_tcp + m_k_BA_tcp + m_dw_tcp_C)
-
- return matrix
def r2eff_ns_mmq_2site_mq(M0=None, F_vector=array([1, 0], float64), m1=None,
m2=None, R20A=None, R20B=None, pA=None, dw=None, dwH=None, kex=None,
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
@@ -213,9 +120,9 @@
# Populate the m1 and m2 matrices (only once per function call for
speed).
# D+ matrix component.
- m1_mat = populate_matrix_rankN(R20A=R20A, R20B=R20B, dw=-dw - dwH,
k_AB=k_AB, k_BA=k_BA, tcp=tcp)
+ m1_mat = rmmq_2site_rankN(R20A=R20A, R20B=R20B, dw=-dw - dwH, k_AB=k_AB,
k_BA=k_BA, tcp=tcp)
# Z- matrix component.
- m2_mat = populate_matrix_rankN(R20A=R20A, R20B=R20B, dw=dw - dwH,
k_AB=k_AB, k_BA=k_BA, tcp=tcp)
+ m2_mat = rmmq_2site_rankN(R20A=R20A, R20B=R20B, dw=dw - dwH, k_AB=k_AB,
k_BA=k_BA, tcp=tcp)
# The M1 and M2 matrices.
# Equivalent to D+.
@@ -377,8 +284,8 @@
NS, NM, NO = num_points.shape
# Populate the m1 and m2 matrices (only once per function call for
speed).
- m1_mat = populate_matrix_rankN(R20A=R20A, R20B=R20B, dw=dw, k_AB=k_AB,
k_BA=k_BA, tcp=tcp)
- m2_mat = populate_matrix_rankN(R20A=R20A, R20B=R20B, dw=-dw, k_AB=k_AB,
k_BA=k_BA, tcp=tcp)
+ m1_mat = rmmq_2site_rankN(R20A=R20A, R20B=R20B, dw=dw, k_AB=k_AB,
k_BA=k_BA, tcp=tcp)
+ m2_mat = rmmq_2site_rankN(R20A=R20A, R20B=R20B, dw=-dw, k_AB=k_AB,
k_BA=k_BA, tcp=tcp)
# The A+/- matrices.
A_pos_mat = matrix_exponential_rankN(m1_mat, dtype=complex64)
r24205 - /branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py