As with the NS CPMG 2-site 3D model, you can shift all of the m_* matrices out of the function so they are initialised only once when relax starts, and not for each function call.
Cheers, Edward On 20 June 2014 08:11, <[email protected]> wrote: > 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): > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
