Re: r24265 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py -- June 24, 2014

Hi Troels,

I've finished the small changes for the dispersion model profiling
master script and am running some speed tests for the various relax
3.1.x versions.  I won't make any more changes except for maybe adding
some new log files as they complete every 2 hours, so it won't get in
your way.  Feel free to add the new models to the master script.  I
had to use svnmerge.py to bring in changes from the relax trunk so
that the output from the master script are better formatted.  So make
sure you update your copy with these changes.

Regards,

Edward



On 24 June 2014 10:43,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Tue Jun 24 10:43:06 2014
New Revision: 24265

URL: http://svn.gna.org/viewcvs/relax?rev=24265&view=rev
Log:
Modified profiling script for NS R1rho 3site, to be functional.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion 
models for Clustered analysis.

Modified:
    
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py?rev=24265&r1=24264&r2=24265&view=diff
==============================================================================
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
    (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py
    Tue Jun 24 10:43:06 2014
@@ -54,7 +54,7 @@
 # relax module imports.
 from lib.physical_constants import g1H, g15N
 from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO, 
MODEL_NS_R1RHO_3SITE
+from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO, 
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR


 # Alter setup.
@@ -109,7 +109,7 @@
     Class Profile inherits the Dispersion container class object.
     """

-    def __init__(self, num_spins=1, model=None, r2=None, r2a=None, 
r2b=None, phi_ex=None, dw=None, pA=None, kex=None, spins_params=None):
+    def __init__(self, num_spins=1, model=None, r2=None, r2a=None, 
r2b=None, phi_ex=None, dw=None, dw_AB=None, dw_BC=None, pA=None, kex=None, 
kex_AB=None, pB=None, kex_BC=None, kex_AC=None, spins_params=None):
         """
         Special method __init__() is called first (acts as Constructor).
         It brings in data from outside the class like the variable 
num_spins.
@@ -172,7 +172,7 @@
         self.chemical_shift = 1.0

         # Assemble param vector.
-        self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
phi_ex=phi_ex, dw=dw, pA=pA, kex=kex, spins_params=spins_params)
+        self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
phi_ex=phi_ex, dw=dw, dw_AB=dw_AB, dw_BC=dw_BC, pA=pA, kex=kex, 
kex_AB=kex_AB, pB=pB, kex_BC=kex_BC, kex_AC=kex_AC, 
spins_params=spins_params)

         # Make nested list arrays of data. And return them.
         values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times, 
offsets, spin_lock_nu1 = self.return_r2eff_arrays()
@@ -402,7 +402,7 @@
         return values, errors, None, missing, frqs, exp_types, 
relax_times, offsets, asarray(spin_lock_nu1)


-    def assemble_param_vector(self, r2=None, r2a=None, r2b=None, 
phi_ex=None, dw=None, pA=None, kex=None, spins_params=None):
+    def assemble_param_vector(self, r2=None, r2a=None, r2b=None, 
phi_ex=None, dw=None, dw_AB=None, dw_BC=None, pA=None, kex=None, 
kex_AB=None, pB=None, kex_BC=None, kex_AC=None, spins_params=None):
         """Assemble the dispersion relaxation dispersion curve fitting 
parameter vector.

         @keyword r2:            The transversal relaxation rate.
@@ -443,10 +443,22 @@
                 value = phi_ex + spin_index
             elif param_name == 'dw':
                 value = dw + spin_index
+            elif param_name == 'dw_AB':
+                value = dw_AB + spin_index
+            elif param_name == 'dw_BC':
+                value = dw_BC + spin_index
             elif param_name == 'pA':
                 value = pA
             elif param_name == 'kex':
                 value = kex
+            elif param_name == 'kex_AB':
+                value = kex_AB
+            elif param_name == 'pB':
+                value = pB
+            elif param_name == 'kex_BC':
+                value = kex_BC
+            elif param_name == 'kex_AC':
+                value = kex_AC

             # Add to the vector.
             param_vector.append(value)
@@ -502,15 +514,31 @@
                 yield 'padw2', pspin_index, 0
             if 'dw' in spins_params:
                 yield 'dw', spin_index, 0
+            if 'dw_AB' in spins_params:
+                yield 'dw_AB', spin_index, 0
+            if 'dw_BC' in spins_params:
+                yield 'dw_BC', spin_index, 0

         # All other parameters (one per spin cluster).
         for param in spins_params:
             if not param in ['r2', 'r2a', 'r2b', 'phi_ex', 'phi_ex_B', 
'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB', 'dwH', 'dwH_AB', 
'dwH_BC', 'dwH_AB']:
                 if param == 'pA':
                     yield 'pA', 0, 0
+
                 elif param == 'kex':
                     yield 'kex', 0, 0

+                elif param == 'kex_AB':
+                    yield 'kex_AB', 0, 0
+
+                elif param == 'pB':
+                    yield 'pB', 0, 0
+
+                elif param == 'kex_BC':
+                    yield 'kex_BC', 0, 0
+
+                elif param == 'kex_AC':
+                    yield 'kex_AC', 0, 0

     def calc(self, params):
         """Calculate chi2 values.
@@ -522,11 +550,11 @@
         """

         # Return chi2 value.
-        chi2 = self.model.func_ns_r1rho_2site(params)
+        chi2 = self.model.func_ns_r1rho_3site(params)
         return chi2


-def single(num_spins=1, model=MODEL_NS_R1RHO_2SITE, iter=None):
+def single(num_spins=1, model=MODEL_NS_R1RHO_3SITE, iter=None):
     """Calculate for a single spin.

     @keyword num_spins:     Number of spins in the cluster.
@@ -540,7 +568,7 @@
     """

     # Instantiate class
-    C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+    C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0, 
dw_BC=2.0, pA=0.8, kex_AB=5000.0, pB=0.1, kex_BC=3000.0, kex_AC=1000.0, 
spins_params=['r2', 'dw_AB', 'dw_BC', 'pA', 'kex_AB', 'pB', 'kex_BC', 
'kex_AC'])

     # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
     for spin_index in xrange(100):
@@ -550,7 +578,7 @@
     print("chi2 single:", chi2)


-def cluster(num_spins=100, model=MODEL_NS_R1RHO_2SITE, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_R1RHO_3SITE, iter=None):
     """Calculate for a number of clustered spins.

     @keyword num_spins:     Number of spins in the cluster.
@@ -564,7 +592,7 @@
     """

     # Instantiate class
-    C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+    C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw_AB=1.0, 
dw_BC=2.0, pA=0.8, kex_AB=5000.0, pB=0.1, kex_BC=3000.0, kex_AC=1000.0, 
spins_params=['r2', 'dw_AB', 'dw_BC', 'pA', 'kex_AB', 'pB', 'kex_BC', 
'kex_AC'])

     # Repeat the function call, to simulate minimisation.
     for i in xrange(iter):


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Re: r24265 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_3site.py

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