Author: tlinnet
Date: Fri Jun 20 15:22:19 2014
New Revision: 24204
URL: http://svn.gna.org/viewcvs/relax?rev=24204&view=rev
Log:
Moved the Bloch-McConnell matrix for 2-site exchange into
lib/dispersion/ns_matrices.py.
This is for consistency with the other 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
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=24204&r1=24203&r2=24204&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_matrices.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_matrices.py Fri Jun 20
15:22:19 2014
@@ -417,6 +417,99 @@
# Return the matrixes.
return R_mat, cR2_mat, Rr_mat, Rex_mat, RCS_mat
+
+def rmmq_2site(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 rmmq_2site_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 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):
r24204 - /branches/disp_spin_speed/lib/dispersion/ns_matrices.py