Author: tlinnet
Date: Fri Jun 20 17:42:51 2014
New Revision: 24209
URL: http://svn.gna.org/viewcvs/relax?rev=24209&view=rev
Log:
Implemented the Bloch-McConnell matrix for 3-site exchange, for
multidimensional data.
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=24209&r1=24208&r2=24209&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_matrices.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_matrices.py Fri Jun 20
17:42:51 2014
@@ -519,6 +519,49 @@
@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: float
+ @keyword R20B: The transverse, spin-spin relaxation rate for
state B.
+ @type R20B: float
+ @keyword R20C: The transverse, spin-spin relaxation rate for
state C.
+ @type R20C: float
+ @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: float
+ @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: 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
+ @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 rmmq_3site_rankN(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,
tcp=None):
+ """The Bloch-McConnell matrix for 3-site exchange.
+
+ @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]
@@ -540,22 +583,124 @@
@type k_AC: float
@keyword k_CA: The rate of exchange from site C to A (rad/s).
@type k_CA: float
+ @keyword tcp: The tau_CPMG times (1 / 4.nu1).
+ @type tcp: numpy float array of rank [NE][NS][NM][NO][ND]
"""
# The first row.
- matrix[0, 0] = -k_AB - k_AC - R20A
- matrix[0, 1] = k_BA
- matrix[0, 2] = k_CA
+ #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
+ #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
+ #matrix[2, 0] = k_AC
+ #matrix[2, 1] = k_BC
+ #matrix[2, 2] = -k_CB - k_CA + 1.j*dw_AC - R20C
+
+ # Pre-multiply with tcp.
+ r20a_tcp = R20A * tcp
+ r20b_tcp = R20B * tcp
+ r20c_tcp = R20C * tcp
+
+ # Complex dw.
+ dw_AB_C_tcp = dw_AB * tcp * 1j
+ dw_AC_C_tcp = dw_AC * tcp * 1j
+
+ k_AB_tcp = k_AB * tcp
+ k_BA_tcp = k_BA * tcp
+ k_BC_tcp = k_BC * tcp
+ k_CB_tcp = k_CB * tcp
+ k_AC_tcp = k_AC * tcp
+ k_CA_tcp = k_CA * tcp
+
+ # R20.
+ m_r20a = array([
+ [-1.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0]])
+
+ m_r20b = array([
+ [0.0, 0.0, 0.0],
+ [0.0, -1.0, 0.0],
+ [0.0, 0.0, 0.0]])
+
+ m_r20c = array([
+ [0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0],
+ [0.0, 0.0, -1.0]])
+
+ # dw.
+ m_dw_AB = array([
+ [0.0, 0.0, 0.0],
+ [0.0, 1.0, 0.0],
+ [0.0, 0.0, 0.0]])
+
+ m_dw_AC = array([
+ [0.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0],
+ [0.0, 0.0, 1.0]])
+
+ # k_x.
+ m_k_AB = array([
+ [-1.0, 0.0, 0.0],
+ [1.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0]])
+
+ m_k_BA = array([
+ [0.0, 1.0, 0.0],
+ [0.0, -1.0, 0.0],
+ [0.0, 0.0, 0.0]])
+
+ m_k_BC = array([
+ [0.0, 0.0, 0.0],
+ [0.0, -1.0, 0.0],
+ [0.0, 1.0, 0.0]])
+
+ m_k_CB = array([
+ [0.0, 0.0, 0.0],
+ [0.0, 0.0, 1.0],
+ [0.0, 0.0, -1.0]])
+
+ m_k_AC = array([
+ [-1.0, 0.0, 0.0],
+ [0.0, 0.0, 0.0],
+ [1.0, 0.0, 0.0]])
+
+ m_k_CA = array([
+ [0.0, 0.0, 1.0],
+ [0.0, 0.0, 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 )
+ m_r20c_tcp = multiply.outer( r20c_tcp, m_r20c )
+
+ # Multiply and expand.
+ m_dw_AB_C_tcp = multiply.outer( dw_AB_C_tcp, m_dw_AB )
+ m_dw_AC_C_tcp = multiply.outer( dw_AC_C_tcp, m_dw_AC )
+
+ # 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 )
+ m_k_BC_tcp = multiply.outer( k_BC_tcp, m_k_BC )
+ m_k_CB_tcp = multiply.outer( k_CB_tcp, m_k_CB )
+ m_k_AC_tcp = multiply.outer( k_AC_tcp, m_k_AC )
+ m_k_CA_tcp = multiply.outer( k_CA_tcp, m_k_CA )
+
+ # Collect matrix.
+ matrix = (m_r20a_tcp + m_r20b_tcp + m_r20c_tcp
+ + m_dw_AB_C_tcp + m_dw_AC_C_tcp
+ + m_k_AB_tcp + m_k_BA_tcp + m_k_BC_tcp
+ + m_k_CB_tcp + m_k_AC_tcp + m_k_CA_tcp)
+
+ 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):
r24209 - /branches/disp_spin_speed/lib/dispersion/ns_matrices.py