r24088 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py -- June 18, 2014 - 15:20

Author: bugman
Date: Wed Jun 18 15:20:11 2014
New Revision: 24088

URL: http://svn.gna.org/viewcvs/relax?rev=24088&view=rev
Log:
Added a script for profiling the 'NS CPMG 2-site 3D' relaxation dispersion 
model.

This is the model at http://wiki.nmr-relax.com/NS_CPMG_2-site_3D.  Again this 
only involved copying
one of the other scripts and modifying a few variable and function names.


Added:
    
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
      - copied, changed from r24085, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py

Copied: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
 (from r24085, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py)
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py?p2=branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py&p1=branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py&r1=24085&r2=24088&rev=24088&view=diff
==============================================================================
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
    (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  Wed Jun 18 15:20:11 2014
@@ -55,14 +55,14 @@
 from lib.physical_constants import g1H, g15N
 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_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
 
 
 # Alter setup.
 def main():
     if True:
         # Nr of iterations.
-        nr_iter = 1000
+        nr_iter = 100
 
         # Print statistics.
         verbose = True
@@ -189,7 +189,7 @@
         end_index = []
         # The spin and frequency dependent R2 parameters.
         end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-        if self.model in [MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
+        if self.model in [MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_3D, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
             end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
         # The spin and dependent parameters (phi_ex, dw, padw2).
         end_index.append(end_index[-1] + self.num_spins)
@@ -424,11 +424,11 @@
         """
 
         # Return chi2 value.
-        chi2 = self.model.func_ns_cpmg_2site_expanded(params)
+        chi2 = self.model.func_ns_cpmg_2site_3D(params)
         return chi2
 
 
-def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_EXPANDED, iter=None):
+def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D, iter=None):
     """Calculate for a single spin.
 
     @keyword num_spins:     Number of spins in the cluster.
@@ -444,13 +444,15 @@
     # Instantiate class
     C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, 
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
 
-    # Repeat the function call, to simulate minimisation.
-    for i in xrange(iter):
-        chi2 = C1.calc(C1.params)
+    # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
+    for spin_index in xrange(100):
+        # Repeat the function call, to simulate minimisation.
+        for i in xrange(iter):
+            chi2 = C1.calc(C1.params)
     print("chi2 single:", chi2)
 
 
-def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_EXPANDED, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_3D, iter=None):
     """Calculate for a number of clustered spins.
 
     @keyword num_spins:     Number of spins in the cluster.
@@ -477,7 +479,7 @@
     main()
 
 def test_reshape():
-    C1 = Profile(num_spins=1, model=MODEL_NS_CPMG_2SITE_EXPANDED, 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_NS_CPMG_2SITE_3D, 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