r23848 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py -- June 11, 2014 - 19:37

Author: tlinnet
Date: Wed Jun 11 19:37:37 2014
New Revision: 23848

URL: http://svn.gna.org/viewcvs/relax?rev=23848&view=rev
Log:
Modified profiling script for the B14 model.

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_b14.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py?rev=23848&r1=23847&r2=23848&view=diff
==============================================================================
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
       (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
       Wed Jun 11 19:37:37 2014
@@ -45,7 +45,7 @@
 
 # relax module imports.
 from lib.physical_constants import g1H, g15N
-from lib.dispersion.cr72 import r2eff_CR72
+from lib.dispersion.b14 import r2eff_B14
 from target_functions.chi2 import chi2
 from target_functions.relax_disp import Dispersion
 from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
@@ -55,7 +55,7 @@
 def main():
     if True:
         # Nr of iterations.
-        nr_iter = 1
+        nr_iter = 100
 
         # Print statistics.
         verbose = True
@@ -144,10 +144,12 @@
 
         # Required data structures.
         self.relax_times = self.fields / (100 * 100. *1E6 )
+        self.inv_relax_times = 1.0 / self.relax_times
         self.ncycs = []
         self.points = []
         self.value = []
         self.error = []
+        self.tau_cpmg_list = []
         for i in range(len(self.fields)):
             ncyc = arange(2, 1000. * self.relax_times[i], 4)
             #ncyc = arange(2, 42, 2)
@@ -155,6 +157,9 @@
             print("sfrq: ", self.fields[i], "number of cpmg frq", len(ncyc), 
ncyc)
 
             cpmg_point = ncyc / self.relax_times[i]
+            tau_cpmg = 0.25 / cpmg_point
+
+            self.tau_cpmg_list.append(list(tau_cpmg))
 
             self.points.append(list(cpmg_point))
             self.value.append([2.0]*len(cpmg_point))
@@ -194,6 +199,9 @@
         dw = self.params[end_index[1]:end_index[2]]
         pA = self.params[end_index[2]]
         kex = self.params[end_index[2]+1]
+        pB = 1.0 - pA
+        k_BA = pA * kex
+        k_AB = pB * kex
 
         # Initialise the data structures for the target function.
         exp_types = []
@@ -275,7 +283,8 @@
                     back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
                     # Initialise call to function.
-                    r2eff_CR72(r20a=r20a, r20b=r20b, pA=pA, dw=dw_frq, 
kex=kex, cpmg_frqs=array(cpmg_frqs[ei][mi][oi]), back_calc=back_calc, 
num_points=len(back_calc))
+                    #r2eff_B14(r20a=r20a, r20b=r20b, pA=pA, dw=dw_frq, 
kex=kex, k_AB=None, k_BA=None, cpmg_frqs=array(cpmg_frqs[ei][mi][oi]), 
back_calc=back_calc, num_points=len(back_calc))
+                    r2eff_B14(r20a=r20a, r20b=r20b, pA=pA, pB=pB, dw=dw_frq, 
kex=kex, k_AB=k_AB, k_BA=k_BA, ncyc=array(self.ncycs[mi]), 
inv_tcpmg=self.inv_relax_times[mi], tcp=array(self.tau_cpmg_list[mi]), 
back_calc=back_calc, num_points=len(back_calc))
 
                     for oi in range(len(self.offset)):
                         for di in range(len(self.points[mi])):
@@ -420,11 +429,11 @@
         """
 
         # Return chi2 value.
-        chi2 = self.model.func_CR72_full(params)
+        chi2 = self.model.func_B14_full(params)
         return chi2
 
 
-def single(num_spins=1, model=MODEL_CR72_FULL, iter=None):
+def single(num_spins=1, model=MODEL_B14_FULL, iter=None):
     """Calculate for a single spin.
 
     @keyword num_spins:     Number of spins in the cluster.
@@ -446,7 +455,7 @@
     print("chi2 single:", chi2)
 
 
-def cluster(num_spins=100, model=MODEL_CR72_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_B14_FULL, iter=None):
     """Calculate for a number of clustered spins.
 
     @keyword num_spins:     Number of spins in the cluster.
@@ -473,7 +482,7 @@
     main()
 
 def test_reshape():
-    C1 = Profile(num_spins=1, model=MODEL_CR72_FULL, r2a=5.0, r2b=10.0, 
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+    C1 = Profile(num_spins=1, model=MODEL_B14_FULL, r2a=5.0, r2b=10.0, 
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
     end_index = C1.model.end_index
     #print("end_index:", end_index)
     num_spins = C1.model.num_spins