r18246 - in /branches/frame_order_testing: ./ specific_fns/ test_suite/system_tests/scripts/n_state_model/ -- January 21, 2013 - 21:18

Author: bugman
Date: Mon Jan 21 21:18:40 2013
New Revision: 18246

URL: http://svn.gna.org/viewcvs/relax?rev=18246&view=rev
Log:
Merged revisions 18244-18245 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk

........
  r18244 | bugman | 2013-01-21 21:01:41 +0100 (Mon, 21 Jan 2013) | 6 lines
  
  Activated the Monte Carlo simulations in the metal_pos_opt.py system test 
script.
  
  This is to test the combination of Monte Carlo simulations and paramagnetic 
centre position
  optimisation.
........
  r18245 | bugman | 2013-01-21 21:17:37 +0100 (Mon, 21 Jan 2013) | 3 lines
  
  Fixes for the support of the paramagnetic centre optimisation during Monte 
Carlo simulations.
........

Modified:
    branches/frame_order_testing/   (props changed)
    branches/frame_order_testing/specific_fns/n_state_model.py
    
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py

Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Jan 21 21:18:40 2013
@@ -1,1 +1,1 @@
-/trunk:1-18242
+/trunk:1-18245

Modified: branches/frame_order_testing/specific_fns/n_state_model.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/n_state_model.py?rev=18246&r1=18245&r2=18246&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/n_state_model.py (original)
+++ branches/frame_order_testing/specific_fns/n_state_model.py Mon Jan 21 
21:18:40 2013
@@ -151,19 +151,18 @@
         # The paramagnetic centre.
         if hasattr(cdp, 'paramag_centre_fixed') and not 
cdp.paramag_centre_fixed:
             if not hasattr(cdp, 'paramagnetic_centre'):
-                param_vector.append(0.0)
-                param_vector.append(0.0)
-                param_vector.append(0.0)
-
+                for i in range(3):
+                    param_vector.append(0.0)
             elif sim_index != None:
-                
param_vector.append(cdp.paramagnetic_centre_sim[sim_index][0])
-                
param_vector.append(cdp.paramagnetic_centre_sim[sim_index][1])
-                
param_vector.append(cdp.paramagnetic_centre_sim[sim_index][2])
-
+                if cdp.paramagnetic_centre_sim[sim_index] == None:
+                    for i in range(3):
+                        param_vector.append(0.0)
+                else:
+                    for i in range(3):
+                        
param_vector.append(cdp.paramagnetic_centre_sim[sim_index][i])
             else:
-                param_vector.append(cdp.paramagnetic_centre[0])
-                param_vector.append(cdp.paramagnetic_centre[1])
-                param_vector.append(cdp.paramagnetic_centre[2])
+                for i in range(3):
+                    param_vector.append(cdp.paramagnetic_centre[i])
 
         # Convert all None values to zero (to avoid conversion to NaN).
         for i in range(len(param_vector)):
@@ -643,6 +642,8 @@
 
             # Monte Carlo simulated positions.
             else:
+                if cdp.paramagnetic_centre_sim[sim_index] == None:
+                    cdp.paramagnetic_centre_sim[sim_index] = [None, None, 
None]
                 cdp.paramagnetic_centre_sim[sim_index][0] = param_vector[-3]
                 cdp.paramagnetic_centre_sim[sim_index][1] = param_vector[-2]
                 cdp.paramagnetic_centre_sim[sim_index][2] = param_vector[-1]
@@ -895,13 +896,15 @@
         atomic_pos = array(atomic_pos, float64)
 
         # The paramagnetic centre.
-        if hasattr(cdp, 'paramagnetic_centre'):
-            if sim_index != None and hasattr(cdp, 'paramag_centre_fixed') 
and not cdp.paramag_centre_fixed:
+        if not hasattr(cdp, 'paramagnetic_centre'):
+            paramag_centre = zeros(3, float64)
+        elif sim_index != None:
+            if cdp.paramagnetic_centre_sim[sim_index] == None:
+                paramag_centre = zeros(3, float64)
+            else:
                 paramag_centre = 
array(cdp.paramagnetic_centre_sim[sim_index])
-            else:
-                paramag_centre = array(cdp.paramagnetic_centre)
         else:
-            paramag_centre = zeros(3, float64)
+            paramag_centre = array(cdp.paramagnetic_centre)
 
         # Return the data structures.
         return atomic_pos, paramag_centre

Modified: 
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py?rev=18246&r1=18245&r2=18246&view=diff
==============================================================================
--- 
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
 (original)
+++ 
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
 Mon Jan 21 21:18:40 2013
@@ -13,7 +13,7 @@
 
 # Set up.
 NUM_STR = 3
-SIMS = False
+SIMS = True
 
 # Path of the alignment data and structure.
 DATA_PATH = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'metal_pos_opt'
@@ -148,7 +148,11 @@
 
 # Monte Carlo simulations.
 if SIMS:
-    self._execute_uf(uf_name='monte_carlo.setup', num=3)
+    # Set up the errors needed for the simulations.
+    self._execute_uf(uf_name='rdc.set_errors', sd=1.0)
+    self._execute_uf(uf_name='pcs.set_errors', sd=0.1)
+
+    self._execute_uf(uf_name='monte_carlo.setup', number=3)
     self._execute_uf(uf_name='monte_carlo.create_data')
     self._execute_uf(uf_name='monte_carlo.initial_values')
     self._execute_uf('simplex', constraints=False, max_iter=500, 
uf_name='minimise')