Bug fix in SpatailDensity with settings

Added svg support for MSD

MDANSE/Framework/Jobs/MeanSquareDisplacement.py

@@ -80,7 +80,7 @@ class MeanSquareDisplacement(IJob):
     settings['grouping_level']=('grouping_level',{})
     settings['transmutated_atoms']=('atom_transmutation',{"dependencies":{'trajectory':'trajectory', 'atom_selection':'atom_selection'}})
     settings['weights']=('weights',{})
-    settings['output_files']=('output_files', {"formats":["netcdf","ascii"]})
+    settings['output_files']=('output_files', {"formats":["netcdf","ascii","svg"]})
     settings['running_mode']=('running_mode',{})
             
     def initialize(self):
@@ -119,7 +119,9 @@ class MeanSquareDisplacement(IJob):
                                        step=self.configuration['frames']['step'])
          
         series = self.configuration['projection']["projector"](series)
- 
+        
+        1/0
+         
         msd = mean_square_displacement(series)
                 
         return index, msd

MDANSE/Framework/Jobs/SpatialDensity.py

@@ -66,9 +66,9 @@ class SpatialDensity(IJob):
     settings['trajectory'] = ('mmtk_trajectory', {'default':os.path.join('..','..','..','Data','Trajectories', 'MMTK', 'protein_in_periodic_universe.nc')})
     settings['frames'] = ('frames', {'dependencies':{'trajectory':'trajectory'}})
     settings['spatial_resolution'] = ('float', {'mini':0.01, 'default':0.1})
-    settings['reference_basis'] = ('basis_selection', {'dependencies':{'trajectory':'trajectory'},
-                                                       'nAtoms':3,
-                                                       'default':('C284H438N84O79S7',('O','C_beta','C_delta'))})
+    settings['reference_basis'] = ('atoms_list', {'dependencies':{'trajectory':'trajectory'},
+                                                  'nAtoms':3,
+                                                  'default':('C284H438N84O79S7',('O','C_beta','C_delta'))})
     settings['target_molecule'] = ('atom_selection', {'dependencies':{'trajectory':'trajectory'},
                                                       'default':'atom_index 151'})
     settings['output_files'] = ('output_files', {'formats':["netcdf","ascii"]})