Merge branch 'bugfix-fix_vacf_normalization_ccf_q_vectors_and_initial_time_issues' into 'develop'

Bugfix fix vacf normalization ccf q vectors and initial time issues

See merge request !33

CHANGELOG

@@ -2,10 +2,12 @@ version 1.2.0
 --------------
 * ADDED issue #27 Better error handling when an error occurs when running an analysis from the GUI
 * ADDED issue #10 Implemented Gromacs trajectory converter
+* FIXED issue #30 Normalization of VACF total value was incorrect
+* FIXED issue #29 Some jobs (AC, CCF, DOS, DACF, DCSF, DISF, GACF, MSD, PACF, RMSD, VACF) did not behave properly if first time of the MD is not zero
 * FIXED issue #28 The time step is now part of the settings for DCD based converters
 * FIXED issue #26 Data can be deleted from the GUI
 * FIXED issue #25 The plotter is now compliant with all matplotlib versions (was crashing on ubuntu-xenial)
-* FIXED issue #25 The plotter is now compliant with all matplotlib versions (was crashing on ubuntu-xenial)
+* FIXED issue #24 Q vectors in CCF Job were incorrect
 * FIXED issue #21 "Save a template for new analysis" button produced an error
 * FIXED issue #20 Opening the theoretical help on MacOS is now OK
 * FIXED issue #18 The items of the checkable combobox are now checkable on Windows

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')
@@ -128,11 +128,7 @@ class CurrentCorrelationFunction(IJob):
             traj = self.configuration['trajectory']['instance']
             
             qVectors = self.configuration["q_vectors"]["value"][shell]["q_vectors"]
-            
-            qVectors = traj.universe._boxToRealPointArray(qVectors.T)
-                                     
-            qVectors = qVectors.T
-            
+                        
             nQVectors = qVectors.shape[1]
             
             rho = {}

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')
@@ -127,11 +127,11 @@ class DynamicCoherentStructureFactor(IJob):
             traj = self.configuration['trajectory']['instance']
             
             qVectors = self.configuration["q_vectors"]["value"][shell]["q_vectors"]
-            
+                        
             qVectors = traj.universe._boxToRealPointArray(qVectors.T)
-                                     
+    
             qVectors = qVectors.T
-                                                            
+                                                                        
             rho = {}
             for element in self.configuration['atom_selection']['unique_names']:
                 rho[element] = numpy.zeros((self._nFrames, qVectors.shape[1]), dtype = numpy.complex64)
@@ -140,7 +140,7 @@ class DynamicCoherentStructureFactor(IJob):
             for i, frame in enumerate(self.configuration['frames']['value']):
                 
                 conf = traj.configuration[frame]
-
+                
                 conf.convertToBoxCoordinates()
 
                 for element,idxs in self._indexesPerElement.items():

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))
@@ -53,6 +50,10 @@ class OutputData(collections.OrderedDict):
         
         for fmt in formats:  
             REGISTRY["format"][fmt].write(basename, self, header)
+            
+    def __setitem__(self, item, value):
+        # Explicitely discard any changes on output data
+        pass
 
 class IOutputVariable(numpy.ndarray):
     '''