[bug #22146] Unpacking of R2A and R2B is performed wrong for clustered "full" dispersion models -- June 06, 2014 - 11:08

URL:
  <http://gna.org/bugs/?22146>

                 Summary: Unpacking of R2A and R2B is performed wrong for
clustered "full" dispersion models 
                 Project: relax
            Submitted by: tlinnet
            Submitted on: Fri 06 Jun 2014 09:08:58 AM UTC
                Category: relax's source code
Specific analysis category: Relaxation dispersion
                Priority: 9 - Immediate
                Severity: 4 - Important
                  Status: None
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: Repository: trunk
         Discussion Lock: Any
        Operating System: All systems

    _______________________________________________________

Details:

The unpacking of the R2A and R2B parameters in the "full" model is performed
wrong.
This will happen performing a clustered analysis, using one of the "full"
models.

This bug affect all analysis performed running with a "full" model, with
clustered residues.

The bug is located in the target function:
./target_functions/relax_disp.py

For all the "func_MODEL_full", the unpacking of:
R20A = params[:self.end_index[0]]
R20B = params[self.end_index[0]:self.end_index[1]]

This is wrong, since the "params" list, is ordered:
[spin, spin, spin, [dw], pA, kex], where spin = [nr_frq*r2a, nr_frq*r2b]

This ordering happens in:
./specific_analysis/relax_disp/parameters.py
in the loop_parameters.py

A possible solutions i shown below.
This alter the unpacking of the parameters.

An example of profiling_cr72.py is attached.
This can be downloaded, and run in base folder of relax:
./profiling_cr72.py .

This is with 3 frq, and 3 spins.

The current implementations would unpack:
('R20A', array([  2.,   2.,   2.,   4.,   4.,   4.,  12.,  12.,  12.]), 9)
('R20B', array([ 14.,  14.,  14.,  22.,  22.,  22.,  24.,  24.,  24.]), 9)

R2A is 2, 12, 22 for the spins 0-3 
R2B is, 4, 14, 24 for the spins 0-3

The suggested unpacking loop, unpacks to:
('R20A', array([  2.,   2.,   2.,  12.,  12.,  12.,  22.,  22.,  22.]), 9)
('R20B', array([  4.,   4.,   4.,  14.,  14.,  14.,  24.,  24.,  24.]), 9)


-------
from numpy import array, concatenate, delete, index_exp
import numpy

p = array([  1.000000000000000e+01, 1.000000000000000e+01,
1.100000000000000e+01
, 1.100000000000000e+01, 1.000000000000000e+01, 1.000000000000000e+01
, 1.100000000000000e+01, 1.100000000000000e+01, 1.000000000000000e+00
, 1.000000000000000e+00, 9.000000000000000e-01, 1.000000000000000e+03])

e = [4, 8, 10]

# Now
r2a = p[:e[0]]
print r2a
r2b = p[e[0]:e[1]]
print r2b
dw = p[e[1]:e[2]]
print dw
pA = p[e[2]]
print pA
kex = p[e[2]+1]
print kex

print "new"
ns = 2
nf = 2

ml = p[:e[1]]

R20A = array([])
R20B = array([])
for i in range(0, ns):
    # Array sorted per [spin, spin, spin], where spin = [nr_frq*r2a,
nr_frq*r2b]
    spin_AB = ml[:nf*2]
    ml = delete(ml, numpy.s_[:nf*2])
    R20A = concatenate([R20A, spin_AB[:nf] ])
    R20B = concatenate([R20B, spin_AB[nf:] ])

print R20A
print R20B
print dw
print pA
print kex



    _______________________________________________________

File Attachments:


-------------------------------------------------------
Date: Fri 06 Jun 2014 09:08:58 AM UTC  Name: profiling_cr72.py  Size: 17kB  
By: tlinnet

<http://gna.org/bugs/download.php?file_id=20938>

    _______________________________________________________

Reply to this item at:

  <http://gna.org/bugs/?22146>

_______________________________________________
  Message sent via/by Gna!
  http://gna.org/