Author: tlinnet
Date: Fri Jun 20 08:11:47 2014
New Revision: 24175
URL: http://svn.gna.org/viewcvs/relax?rev=24175&view=rev
Log:
Added the function "rcpmg_star_rankN" for the collection of the
multidimensional relaxation matrix for model NS CPMG 2site star.
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=24175&r1=24174&r2=24175&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_matrices.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_matrices.py Fri Jun 20
08:11:47 2014
@@ -31,7 +31,7 @@
# Python module imports.
from math import cos, sin, pi
-from numpy import array, float64, matrix, multiply
+from numpy import add, array, conj, complex64, float64, matrix, multiply
def r180x_2d(flip=pi):
@@ -318,6 +318,105 @@
# Return the matrix.
return c_mat
+
+
+def rcpmg_star_rankN(R2A=None, R2B=None, pA=None, pB=None, dw=None,
k_AB=None, k_BA=None, tcp=None):
+ """Definition of the exchange matrix, for rank
[NE][NS][NM][NO][ND][2][2].
+
+ @keyword R2A: The transverse, spin-spin relaxation rate for state A.
+ @type R2A: numpy float array of rank [NE][NS][NM][NO][ND]
+ @keyword R2B: The transverse, spin-spin relaxation rate for state B.
+ @type R2B: numpy float array of rank [NE][NS][NM][NO][ND]
+ @keyword pA: The population of state A.
+ @type pA: float
+ @keyword pB: The population of state B.
+ @type pB: float
+ @keyword dw: The chemical exchange difference between states A and
B in rad/s.
+ @type dw: numpy float array of rank [NE][NS][NM][NO][ND]
+ @keyword k_AB: The forward exchange rate from state A to state B.
+ @type k_AB: float
+ @keyword k_BA: The reverse exchange rate from state B to state A.
+ @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 R and complex conjugate cR2.
+ @rtype: numpy float array of rank [NE][NS][NM][NO][ND][2][2]
+ """
+
+ # Pre-multiply with tcp.
+ r20a_tcp = R2A * tcp
+ r20b_tcp = R2B * tcp
+ k_AB_tcp = k_AB * tcp
+ k_BA_tcp = k_BA * tcp
+ # Complex dw.
+ dw_tcp_C = dw * tcp * -1j
+
+ # Create matrix for collection of Rr matrix.
+ # The matrix that contains only the R2 relaxation terms ("Redfield
relaxation", i.e. non-exchange broadening).
+ #Rr[0, 0] = -R2A_si_mi
+ #Rr[1, 1] = -R2B_si_mi
+
+ m_r20a = array([
+ [-1.0, 0.0],
+ [0.0, 0.0],], complex64)
+
+ m_r20b = array([
+ [0.0, 0.0],
+ [0.0, -1.0],], complex64)
+
+ # Multiply and expand.
+ m_r20a_tcp = multiply.outer( r20a_tcp, m_r20a )
+ m_r20b_tcp = multiply.outer( r20b_tcp, m_r20b )
+
+ # Collect Rr matrix.
+ Rr_mat = (m_r20a_tcp + m_r20b_tcp)
+
+ # Create matrix for collection of Rex.
+ # Set up the matrix that contains the exchange terms between the two
states A and B.
+ #Rex[0, 0] = -k_AB
+ #Rex[0, 1] = k_BA
+ #Rex[1, 0] = k_AB
+ #Rex[1, 1] = -k_BA
+
+ m_k_AB = array([
+ [-1.0, 0.0],
+ [1.0, 0.0],], complex64)
+
+ m_k_BA = array([
+ [0.0, 1.0],
+ [0.0, -1.0],], complex64)
+
+ # 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 )
+
+ # Collect Rex matrix.
+ Rex_mat = (m_k_AB_tcp + m_k_BA_tcp)
+
+ # Create the matrix for RCS.
+ # The matrix that contains the chemical shift evolution. It works
here only with X magnetization, and the complex notation allows to evolve
in the transverse plane (x, y). The chemical shift for state A is assumed
to be zero.
+ #RCS[1, 1] = complex(0.0, -dw_si_mi)
+
+ m_dw = array([
+ [0.0, 0.0],
+ [0.0, 1.0],], complex64)
+
+ # Multiply and expand.
+ m_dw_tcp_C = multiply.outer( dw_tcp_C, m_dw )
+
+ # Collect RCS matrix.
+ RCS_mat = m_dw_tcp_C
+
+ # The matrix R that contains all the contributions to the evolution,
i.e. relaxation, exchange and chemical shift evolution.
+ R_mat = add(Rr_mat, Rex_mat)
+ R_mat = add(R_mat, RCS_mat)
+
+ # This is the complex conjugate of the above. It allows the chemical
shift to run in the other direction, i.e. it is used to evolve the shift
after a 180 deg pulse. The factor of 2 is to minimise the number of
multiplications for the prop_2 matrix calculation.
+ cR2_mat = conj(R_mat) * 2.0
+
+ # Return the matrixes.
+ return R_mat, cR2_mat, Rr_mat, Rex_mat, RCS_mat
+
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):
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Re: r24175 - /branches/disp_spin_speed/lib/dispersion/ns_matrices.py