Re: r24165 - /branches/disp_spin_speed/lib/dispersion/ns_matrices.py -- June 23, 2014

Hi Troels,

I have a number of points about the lib/dispersion/ns_matrices.py file:

1)  Should the matrices you have introduced here be set to the
numpy.float64 type?

2)  For nicer formatting of the matrices, you could add an extra space
in front of all positive numbers.  If you use the float64 type in the
array() function, you could also drop the '.0' from all numbers.  This
will then be much easier to see.

3)  This lib.dispersion.ns_matrices module is now becoming too big.
Maybe it can be broken up for each model.  I can see that there is no
code sharing at all any more which defeats the purpose of having a
separate ns_matrices module.  So rcpmg_star_rankN() could go into
ns_cpmg_2site_3d_matrices.py or into the module it is used in
ns_cpmg_2site_3d.py, and the same for all other functions.

4)  Shift the fixed matrices out of the function.  All the matrices
you have introduced here can be initialised on import, as they never
change.  Then they will not be created for each function call, saving
some time and memory.  The idea is the same as the hardcoded
"eta_scale = 2.0**(-3.0/2.0)" variable in the CR72 modules.

5)  The final comma can go.  The matrices end with "[0.0, 0.0, 0.0,
0.0, 0.0, -1.0], ])", but this should be "[0.0, 0.0, 0.0, 0.0, 0.0,
-1.0]])".

Cheers,

Edward

On 19 June 2014 20:17,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Thu Jun 19 20:17:47 2014
New Revision: 24165

URL: http://svn.gna.org/viewcvs/relax?rev=24165&view=rev
Log:
Added the ns matrice, rr1rho_3d_rankN, to collect the multi dimensional 3D 
exchange matrix, of rank [NE][NS][NM][NO][ND][6][6].

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=24165&r1=24164&r2=24165&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/dispersion/ns_matrices.py      (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_matrices.py      Thu Jun 19 
20:17:47 2014
@@ -462,3 +462,134 @@
     matrix[3, 0] = k_AB
     matrix[4, 1] = k_AB
     matrix[5, 2] = k_AB
+
+
+def rr1rho_3d_rankN(R1=None, r1rho_prime=None, pA=None, pB=None, dw=None, 
omega=None, offset=None, w1=None, k_AB=None, k_BA=None):
+    """Definition of the multidimensional 3D exchange matrix, of rank 
[NE][NS][NM][NO][ND][6][6].
+
+    This code originates from the funNumrho.m file from the Skrynikov & 
Tollinger code (the sim_all.tar file 
https://gna.org/support/download.php?file_id=18404 attached to 
https://gna.org/task/?7712#comment5).
+
+
+    @keyword R1:            The longitudinal, spin-lattice relaxation rate.
+    @type R1:               numpy float array of rank [NE][NS][NM][NO][ND]
+    @keyword r1rho_prime:   The R1rho transverse, spin-spin relaxation 
rate in the absence of exchange.
+    @type r1rho_prime:      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 [NS][NM][NO][ND]
+    @keyword omega:         The chemical shift for the spin in rad/s.
+    @type omega:            numpy float array of rank [NS][NM][NO][ND]
+    @keyword offset:        The spin-lock offsets for the data.
+    @type offset:           numpy float array of rank [NS][NM][NO][ND]
+    @keyword w1:            The spin-lock field strength in rad/s.
+    @type w1:               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 k_BA:          The reverse exchange rate from state B to 
state A.
+    @type k_BA:             float
+    @return:                The relaxation matrix.
+    @rtype:                 numpy float array of rank 
[NE][NS][NM][NO][ND][6][6]
+    """
+
+    # Wa: The chemical shift offset of state A from the spin-lock. Larmor 
frequency [s^-1].
+    Wa = omega
+    # Wb: The chemical shift offset of state A from the spin-lock. Larmor 
frequency [s^-1].
+    Wb = omega + dw
+
+    # Population-averaged Larmor frequency [s^-1].
+    W = pA*Wa + pB*Wb
+
+    # Offset of spin-lock from A.
+    dA = Wa - offset
+
+    # Offset of spin-lock from B.
+    dB = Wb - offset
+
+    # Offset of spin-lock from population-average.
+    d = W - offset
+
+    wA=dA
+    wB=dB
+
+
+    m_r1rho_prime = array([
+        [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, -1.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], ])
+
+    m_wA = array([
+        [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
+        [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], ])
+
+    m_wB = array([
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
+        [0.0, 0.0, 0.0, 1.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], ])
+
+    m_w1 = array([
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, -1.0],
+        [0.0, 0.0, 0.0, 0.0, 1.0, 0.0], ])
+
+    m_k_AB = array([
+        [-1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, -1.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
+        [1.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 1.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 1.0, 0.0, 0.0, 0.0], ])
+
+    m_k_BA = array([
+        [0.0, 0.0, 0.0, 1.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 1.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 1.0],
+        [0.0, 0.0, 0.0, -1.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, -1.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, -1.0], ])
+
+    m_R1 = array([
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, -1.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, -1.0], ])
+
+    # Multiply and expand.
+    mat_r1rho_prime = multiply.outer( r1rho_prime, m_r1rho_prime )
+
+    mat_wA = multiply.outer( wA, m_wA )
+    mat_wB = multiply.outer( wB, m_wB )
+
+    mat_w1 = multiply.outer( w1, m_w1 )
+
+    mat_k_AB = multiply.outer( k_AB, m_k_AB )
+    mat_k_BA = multiply.outer( k_BA, m_k_BA )
+
+    mat_R1 = multiply.outer( R1, m_R1 )
+
+    # Collect matrix.
+    matrix = (mat_r1rho_prime + mat_wA + mat_wB
+        + mat_w1 + mat_k_AB + mat_k_BA
+        + mat_R1)
+
+    # Return the matrix.
+    return matrix


_______________________________________________
relax (http://www.nmr-relax.com)

This is the relax-commits mailing list
relax-commits@xxxxxxx

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

Re: r24165 - /branches/disp_spin_speed/lib/dispersion/ns_matrices.py

Header

Content

Related Messages