Replacing all output_file occurences by output_files

MDANSE/Framework/Jobs/Castep.py

@@ -142,7 +142,7 @@ class CASTEPConverter(Converter):
         
     settings = collections.OrderedDict()
     settings['castep_file'] = ('input_file', {'default':os.path.join('..','..','..','Data','Trajectories','CASTEP','PBAnew.md')})
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
                 
     def initialize(self):
         """
@@ -165,7 +165,7 @@ class CASTEPConverter(Converter):
         self._gradients = ParticleVector(self._universe)        
 
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w')
 
         # A frame generator is created.
         self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])

MDANSE/Framework/Jobs/DCDConverter.py

@@ -280,7 +280,7 @@ class DCDConverter(Converter):
     settings = collections.OrderedDict()
     settings['pdb_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.pdb')})
     settings['dcd_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','CHARMM','2vb1.dcd')})
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
     settings['fold'] = ('boolean', {'default':False,'label':"Fold coordinates in to box"})    
 
     def initialize(self):
@@ -313,7 +313,7 @@ class DCDConverter(Converter):
         resolve_undefined_molecules_name(self._universe)
         
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w')
         
         # A frame generator is created.        
         self._snapshot = SnapshotGenerator(self._universe, actions=[TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])

MDANSE/Framework/Jobs/DL_POLY.py

@@ -299,7 +299,7 @@ class DL_POLYConverter(Converter):
                                               'default':os.path.join('..','..','..','Data','Trajectories','DL_Poly','HISTORY_cumen')})
     settings['atom_aliases'] = ('python_object',{'default':{}})
     settings['version'] = ('single_choice', {'choices':_HISTORY_FORMAT.keys(), 'default':'2'})
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
                     
     def initialize(self):
         '''
@@ -338,7 +338,7 @@ class DL_POLYConverter(Converter):
             
                         
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w', comment=self._fieldFile["title"])
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w', comment=self._fieldFile["title"])
 
         # A frame generator is created.
         self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])

MDANSE/Framework/Jobs/Discover.py

@@ -235,7 +235,7 @@ class DiscoverConverter(Converter):
     settings = collections.OrderedDict()
     settings['xtd_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','Discover','sushi.xtd')})
     settings['his_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','Discover','sushi.his')})
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
     
     def initialize(self):
         '''
@@ -267,7 +267,7 @@ class DiscoverConverter(Converter):
         self._universe.foldCoordinatesIntoBox()
             
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w', comment=self._hisfile["title"])
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w', comment=self._hisfile["title"])
 
         # A frame generator is created.
         self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])

MDANSE/Framework/Jobs/Forcite.py

@@ -285,7 +285,7 @@ class ForciteConverter(Converter):
     settings = collections.OrderedDict()
     settings['xtd_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','Forcite','nylon66_rho100_500K_v300K.xtd')})
     settings['trj_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','Forcite','nylon66_rho100_500K_v300K.trj')})
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
                 
     def initialize(self):
         '''
@@ -315,7 +315,7 @@ class ForciteConverter(Converter):
             self._forces.array[:,:] = 0.00
 
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w', comment=self._trjfile["title"])
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w', comment=self._trjfile["title"])
 
         # A frame generator is created.
         self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])

MDANSE/Framework/Jobs/Generic.py

@@ -166,7 +166,7 @@ class GenericConverter(Converter):
     settings = collections.OrderedDict()   
     settings['gt_file'] = ('input_file',{'wildcard':"Generic trajectory files|*.gtf|All files|*",
                                          'default':os.path.join('..','..','..','Data','Trajectories','Generic','test.gtf')})
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
                     
     def initialize(self):
         '''
@@ -331,7 +331,7 @@ class GenericConverter(Converter):
             self._dataShape=(self._universe.numberOfAtoms(),3)
                                     
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w')
  
         # A frame generator is created.
         self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])

MDANSE/Framework/Jobs/LAMMPS.py

@@ -140,7 +140,7 @@ class LAMMPSConverter(Converter):
     settings['mass_tolerance'] = ('float', {'label':"mass tolerance (uma)", 'default':1.0e-5, 'mini':1.0e-9})        
     settings['time_step'] = ('float', {'label':"time step (fs)", 'default':1.0, 'mini':1.0e-9})        
     settings['n_steps'] = ('integer', {'label':"number of time steps", 'default':1, 'mini':0})        
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
     
     def initialize(self):
         '''
@@ -155,7 +155,7 @@ class LAMMPSConverter(Converter):
         self.parse_first_step()
         
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w')
 
         self._nameToIndex = dict([(at.name,at.index) for at in self._universe.atomList()])
 

MDANSE/Framework/Jobs/PDB.py

@@ -51,7 +51,7 @@ class PDBConverter(Converter):
     settings['pdb_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','PDB','2f58_nma.pdb')})
     settings['nb_frame'] = ('range', {'valueType':int, 'includeLast':True, 'mini':0.0, 'default':(0,2,1)})
     settings['time_step'] = ('float', {'mini':1.0e-6, 'default':1.0})
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
      
     def initialize(self):
         """
@@ -71,7 +71,7 @@ class PDBConverter(Converter):
         self._universe.addObject(pdb_config.createAll(None, 1))
         
         # Open the new trajectory 
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], "w", "Converted from PDB")
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], "w", "Converted from PDB")
         
         # Make a snapshot generator for saving.
         self._snapshot = SnapshotGenerator(self._universe,actions = [TrajectoryOutput(self._trajectory, None, 0, None, 1)])

MDANSE/Framework/Jobs/VASP.py

@@ -126,7 +126,7 @@ class VASPConverter(Converter):
     settings = collections.OrderedDict()           
     settings['xdatcar_file'] = ('input_file',{'default':os.path.join('..','..','..','Data','Trajectories','VASP','XDATCAR_version5')})
     settings['time_step'] = ('float', {'label':"time step", 'default':1.0, 'mini':1.0e-9})        
-    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+    settings['output_files'] = ('output_files', {'formats':["netcdf"]})
                 
     def initialize(self):
         '''
@@ -146,7 +146,7 @@ class VASPConverter(Converter):
                 self._universe.addObject(Atom(symbol, name="%s_%d" % (symbol,i)))        
 
         # A MMTK trajectory is opened for writing.
-        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
+        self._trajectory = Trajectory(self._universe, self.configuration['output_files']['files'][0], mode='w')
 
         # A frame generator is created.
         self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])

Tests/FunctionalTests/Jobs/BuildJobTests.py

@@ -53,10 +53,7 @@ class JobFileGenerator():
             temp = 'parameters[%r] = %r\n' % (k, v)
             test_string = test_string + '        ' + temp.replace('\\\\', '/')
         test_string = test_string +     '        job = REGISTRY[%r][%r]()\n' % ('job',self.job._type)
-        test_string = test_string +     '        if "output_file" in parameters:\n'
-        test_string = test_string +     '            output_path = parameters["output_file"][0]\n'
-        test_string = test_string +     '        else:\n'
-        test_string = test_string +     '            output_path = parameters["output_files"][0]\n'
+    test_string = test_string +     '            output_path = parameters["output_files"][0]\n'
         test_string = test_string +     '        reference_data_path = "' + self.reference_data_path.replace('\\', '/') + '"\n'
         # Launch the job in monoprocessor mode and copy output file
         test_string = test_string +     '        print "Launching job in monoprocessor mode"\n'