Fix problem with normalization and change from time to duration in analysis...

Fix problem with normalization and change from time to duration in analysis computing correlations between different frames

MDANSE/Framework/Configurators/FramesConfigurator.py

@@ -84,6 +84,8 @@ class FramesConfigurator(RangeConfigurator):
             self['time_step'] = self['time'][1] - self['time'][0]
         except IndexError:
             self['time_step'] = 1.0
+            
+        self['duration'] = self['time'] - self['time'][0]    
 
     def get_information(self):
         '''

MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -85,7 +85,7 @@ class AngularCorrelation(IJob):
                 
         self.numberOfSteps = self.configuration['axis_selection']['n_values']
 
-        self._outputData.add("time","line", self.configuration['frames']['time'],units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'],units='ps')
 
         self._outputData.add("axis_index","line", numpy.arange(self.configuration['axis_selection']['n_values']), units='au')
                         

MDANSE/Framework/Jobs/CurrentCorrelationFunction.py

@@ -85,7 +85,7 @@ class CurrentCorrelationFunction(IJob):
                 
         self._outputData.add("q","line", numpy.array(self.configuration["q_vectors"]["shells"]), units="inv_nm") 
 
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
         self._outputData.add("time_window","line", self._instrResolution["time_window"], units="au") 
 
         self._outputData.add("omega","line", self._instrResolution["omega"],units='rad/ps')

MDANSE/Framework/Jobs/DensityOfStates.py

@@ -73,7 +73,7 @@ class DensityOfStates(IJob):
 
         instrResolution = self.configuration["instrument_resolution"]        
                 
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
         self._outputData.add("time_window","line", instrResolution["time_window"], axis="time", units="au") 
 
         self._outputData.add("omega","line", instrResolution["omega"], units='rad/ps')

MDANSE/Framework/Jobs/DipoleAutoCorrelationFunction.py

@@ -64,7 +64,7 @@ class DipoleAutoCorrelationFunction(IJob):
         self.numberOfSteps = self.configuration['frames']['number']
                         
         # Will store the time.
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
         
         self._dipoleMoments = numpy.zeros((self.configuration['frames']['number'],3),dtype=numpy.float64)
             

MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py

@@ -91,7 +91,7 @@ class DynamicCoherentStructureFactor(IJob):
 
         self._outputData.add("q","line",self.configuration["q_vectors"]["shells"], units="inv_nm") 
 
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
         self._outputData.add("time_window","line", self._instrResolution["time_window"], units="au") 
 
         self._outputData.add("omega","line", self._instrResolution["omega"], units='rad/ps')

MDANSE/Framework/Jobs/DynamicIncoherentStructureFactor.py

@@ -82,7 +82,7 @@ class DynamicIncoherentStructureFactor(IJob):
 
         self._outputData.add("q","line", self.configuration["q_vectors"]["shells"], units="inv_nm") 
 
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
         self._outputData.add("time_window","line", self._instrResolution["time_window"], axis="time", units="au") 
 
         self._outputData.add("omega","line", self._instrResolution["omega"], units='rad/ps')

MDANSE/Framework/Jobs/GaussianDynamicIncoherentStructureFactor.py

@@ -86,7 +86,7 @@ class GaussianDynamicIncoherentStructureFactor(IJob):
 
         self._outputData.add("q2","line",self._kSquare,units="inv_nm**2") 
 
-        self._outputData.add("time","line",self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line",self.configuration['frames']['duration'], units='ps')
         self._outputData.add("time_window","line",self._instrResolution["time_window"], axis="time", units="au") 
 
         self._outputData.add("omega","line",self.configuration["instrument_resolution"]["omega"], units='rad/ps')

MDANSE/Framework/Jobs/GeneralAutoCorrelationFunction.py

@@ -69,7 +69,7 @@ class GeneralAutoCorrelationFunction(IJob):
         self.numberOfSteps = self.configuration['atom_selection']['selection_length']
         
         # Will store the time.
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
 
         # Will store the mean square displacement evolution.
         for element in self.configuration['atom_selection']['unique_names']:

MDANSE/Framework/Jobs/MeanSquareDisplacement.py

@@ -89,7 +89,7 @@ class MeanSquareDisplacement(IJob):
         self.numberOfSteps = self.configuration['atom_selection']['selection_length']
                         
         # Will store the time.
-        self._outputData.add("time", "line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time", "line", self.configuration['frames']['duration'], units='ps')
                         
         # Will store the mean square displacement evolution.
         for element in self.configuration['atom_selection']['unique_names']:

MDANSE/Framework/Jobs/PositionAutoCorrelationFunction.py

@@ -68,7 +68,7 @@ class PositionAutoCorrelationFunction(IJob):
         self.numberOfSteps = self.configuration['atom_selection']['selection_length']
                         
         # Will store the time.
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
                     
         # Will store the mean square displacement evolution.
         for element in self.configuration['atom_selection']['unique_names']:

MDANSE/Framework/Jobs/RootMeanSquareDeviation.py

@@ -72,7 +72,7 @@ class RootMeanSquareDeviation(IJob):
         self._referenceIndex = self.configuration['reference_frame']['value']
         
         # Will store the time.
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
                                     
         # Will store the mean square deviation
         for element in self.configuration['atom_selection']['unique_names']:

MDANSE/Framework/Jobs/VelocityAutoCorrelationFunction.py

@@ -93,7 +93,7 @@ class VelocityAutoCorrelationFunction(IJob):
         self.numberOfSteps = self.configuration['atom_selection']['selection_length']
                         
         # Will store the time.
-        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['duration'], units='ps')
             
         # Will store the mean square displacement evolution.
         for element in self.configuration['atom_selection']['unique_names']:
@@ -160,15 +160,16 @@ class VelocityAutoCorrelationFunction(IJob):
         for element, number in nAtomsPerElement.items():
             self._outputData["vacf_%s" % element] /= number
 
-        if self.configuration['normalize']["value"]:
-            for element in nAtomsPerElement.keys():
-                self._outputData["vacf_%s" % element] = normalize(self._outputData["vacf_%s" % element], axis=0)
-                    
         weights = self.configuration["weights"].get_weights()
                     
         vacfTotal = weight(weights,self._outputData,nAtomsPerElement,1,"vacf_%s")
         self._outputData["vacf_total"][:] = vacfTotal
-                
+        
+        if self.configuration['normalize']["value"]:
+            for element in nAtomsPerElement.keys():
+                self._outputData["vacf_%s" % element] = normalize(self._outputData["vacf_%s" % element], axis=0)
+            self._outputData["vacf_total"] = normalize(self._outputData["vacf_total"], axis=0)
+                                    
         self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         
         self.configuration['trajectory']['instance'].close()     

MDANSE/Framework/OutputVariables/IOutputVariable.py

@@ -42,9 +42,6 @@ class OutputVariableError(Error):
 
 class OutputData(collections.OrderedDict):
     
-    def __setitem__(self,item,value):
-        pass
-    
     def add(self, dataName, dataType, data, **kwargs):
                 
         collections.OrderedDict.__setitem__(self,dataName,REGISTRY["output_variable"][dataType](data, dataName, **kwargs))