The frequencies computed (and displayed) is now an angular frequency

MDANSE/Externals/magnitude/magnitude.py

@@ -342,9 +342,9 @@ def _numberp(n):  ## Python has to have a decent way to do this!
             isinstance(n, types.LongType))
 
 class Magnitude:
-    def __init__(self, val, m=0, s=0, K=0, kg=0, A=0, mol=0, cd=0, dollar=0, b=0):
+    def __init__(self, val, m=0, s=0, K=0, kg=0, A=0, mol=0, cd=0, dollar=0, b=0, rad=0):
         self.val = val
-        self.unit = [m, s, K, kg, A, mol, cd, dollar, b]
+        self.unit = [m, s, K, kg, A, mol, cd, dollar, b, rad]
         self.out_unit = None
         self.out_factor = None
         self.oprec = None
@@ -1059,10 +1059,11 @@ def _init_mags():
     new_mag('$', Magnitude(1.0, dollar=1))
     new_mag('dollar', Magnitude(1.0, dollar=1))
     new_mag('b', Magnitude(1.0, b=1))           # bit
+    new_mag('rad', Magnitude(1.0, rad=1))           # bit
 
     # Magnitudes for derived SI units
     new_mag('B', Magnitude(8.0, b=1))
-    new_mag('rad', Magnitude(1.0))  # radian
+#    new_mag('rad', Magnitude(1.0))  # radian
     new_mag('sr', Magnitude(1.0))  # steradian
     new_mag('Hz', Magnitude(1.0, s=-1))  # hertz
     new_mag('g', Magnitude(1e-3, kg=1))  # gram
@@ -1134,33 +1135,47 @@ def _init_mags():
     new_mag('J_per_mole', Magnitude(1.66055927e-24, m=2, kg=1, s=-2))    
     new_mag('eV', Magnitude(1.60217649e-19, m=2, kg=1, s=-2))
     new_mag('Ha', Magnitude(4.35974394e-18, m=2, kg=1, s=-2))
-    
-    # Eric - frequency
-    new_mag('rad_inv_s', Magnitude(2.0*math.pi, s=-1))
-    
+        
     # Energy equivalent
-    new_mag('inv_m_eq', Magnitude(1.9864455e-25, m=2, kg=1, s=-2))
-    new_mag('Hz_eq', Magnitude(6.62606896e-34, m=2, kg=1, s=-2))
-    new_mag('K_eq', Magnitude(1.3806504e-23, m=2, kg=1, s=-2))
-    new_mag('u_eq', Magnitude(1.49241783e-10, m=2, kg=1, s=-2))
+    new_mag('1/m_eq', Magnitude(1.9864455e-25, m=2, kg=1, s=-2))
+    new_mag('hnu', Magnitude(6.62606896e-34, m=2, kg=1, s=-2))
+    new_mag('T(energy)', Magnitude(1.3806504e-23, m=2, kg=1, s=-2))
+    new_mag('m(energy)', Magnitude(1.49241783e-10, m=2, kg=1, s=-2))
+
+    new_mag('h', Magnitude(6.62607004e-34,m=2,kg=1,s=-1))
+    new_mag('hbar', Magnitude(6.62607004e-34/2.0/math.pi,m=2,kg=1,s=-1,rad=-1))
 
     # Frequency equivalent
-    new_mag('J_eq', Magnitude(1.50919045e+33, s=-1))
-    new_mag('eV_eq', Magnitude(2.41798945e+14, s=-1))
+    new_mag('J(freq)', Magnitude(1.50919045e+33, s=-1))
+    new_mag('eV(freq)', Magnitude(2.41798945e+14, s=-1))
 
     # Eric - inverse of distance
-    new_mag('inv_m', Magnitude(1.0, m=-1, kg=0, s=0))
-    new_mag('inv_m', Magnitude(1.0, m=-1, kg=0, s=0))
-    new_mag('inv_um', Magnitude(1.0e6, m=-1, kg=0, s=0))
-    new_mag('inv_nm', Magnitude(1.0e9, m=-1, kg=0, s=0))
-    new_mag('inv_ang', Magnitude(1.0e10, m=-1, kg=0, s=0))
+#    new_mag('1/m', Magnitude(1.0, m=-1, kg=0, s=0))
+#    new_mag('inv_cm', Magnitude(1.0e2, m=-1, kg=0, s=0))
+#    new_mag('inv_um', Magnitude(1.0e6, m=-1, kg=0, s=0))
+#    new_mag('inv_nm', Magnitude(1.0e9, m=-1, kg=0, s=0))
+#    new_mag('inv_ang', Magnitude(1.0e10, m=-1, kg=0, s=0))
+
+    new_mag('cyc', Magnitude(2.0*math.pi,rad=1))
     
     new_mag('au', Magnitude(1.0))
     new_mag('wu', Magnitude(1.0))
     new_mag('unitless', Magnitude(1.0))
     new_mag('no-unit', Magnitude(1.0))
 
+    # Eric - frequency
+#    new_mag('rad_inv_s', Magnitude(1.0, s=-1))
+#    new_mag('rad_inv_ps', Magnitude(1.0e12, s=-1))
+
 
 if not MAGS:
     _init_mags()
+
+if __name__ == "__main__":
+    print mg(1.0,'h THz','meV')
+    print mg(1.0,'meV/h','THz')
+    print mg(1.0,'hbar rad/ps','meV')
+    print mg(1.0,'cyc THz','rad/ps')
+    print mg(1.0,'rad/ps',' cyc THz')
+    print mg(1.0,'rad/ps',' cyc meV(freq)')
     

MDANSE/Framework/Configurators/InstrumentResolutionConfigurator.py

@@ -33,7 +33,7 @@ Created on Mar 30, 2015
 import numpy
 
 from MDANSE import REGISTRY
-from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
+from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
 class InstrumentResolutionConfigurator(IConfigurator):
     """
@@ -43,7 +43,7 @@ class InstrumentResolutionConfigurator(IConfigurator):
     of states) when performing the fourier transform of its time-dependant counterpart. This allow to 
     convolute of the signal with a resolution function to have a better match with experimental spectrum.
     
-    In MDANSE, the instrument resolution are defined in frequency (energy) space and are internally 
+    In MDANSE, the instrument resolution are defined in omegas space and are internally 
     inverse-fourier-transformed to get a time-dependant version. This time-dependant resolution function will then 
     be multiplied by the time-dependant signal to get the resolution effect according to the Fourier Transform theorem:
     
@@ -83,11 +83,10 @@ class InstrumentResolutionConfigurator(IConfigurator):
         self._timeStep = framesCfg['time'][1] - framesCfg['time'][0]
         self['time_step'] = self._timeStep
                 
-        self["frequencies"] = numpy.fft.fftshift(numpy.fft.fftfreq(2*self["n_frames"]-1,self["time_step"]))
-        
-        df = round(self["frequencies"][1] - self["frequencies"][0],3)
-        
-        self["n_frequencies"] = len(self["frequencies"])
+        # We compute angular frequency AND NOT ORDINARY FREQUENCY ANYMORE
+        self["omega"] = 2.0*numpy.pi*numpy.fft.fftshift(numpy.fft.fftfreq(2*self["n_frames"]-1,self["time_step"]))
+                
+        self["n_omegas"] = len(self["omega"])
 
         kernel, parameters = value
                 
@@ -97,21 +96,11 @@ class InstrumentResolutionConfigurator(IConfigurator):
         
         resolution.setup(parameters)
         
-        resolution.set_kernel(self["frequencies"], self["time_step"])
-
-        dmax = resolution.timeWindow.max()-1
-        
-        if dmax > 0.1:
-            raise ConfiguratorError('''the resolution function is too sharp for the available frequency step. 
-You can change your resolution function settings to make it broader or use "ideal" kernel if you do not want to smooth your signal.
-For a gaussian resolution function, this would correspond to a sigma at least equal to the frequency step (%s)''' % df,self)
-        elif dmax < -0.1:
-            raise ConfiguratorError('''the resolution function is too broad.
-You should change your resolution function settings to make it sharper.''',self)
+        resolution.set_kernel(self["omega"], self["time_step"])
             
-        self["frequency_window"] = resolution.frequencyWindow
+        self["omega_window"] = resolution.omegaWindow
 
-        self["time_window"] = resolution.timeWindow
+        self["time_window"] = resolution.timeWindow.real
         
         self["kernel"] = kernel
         self["parameters"] = parameters

MDANSE/Framework/InstrumentResolutions/GaussianResolution.py

@@ -46,10 +46,10 @@ class GaussianInstrumentResolution(IInstrumentResolution):
     settings['mu'] = ('float', {"default":0.0})
     settings['sigma'] = ('float', {"default":1.0})
 
-    def set_kernel(self, frequencies, dt):
+    def set_kernel(self, omegas, dt):
 
         mu = self._configuration["mu"]["value"]
         sigma = self._configuration["sigma"]["value"]
                         
-        self._frequencyWindow = (numpy.sqrt(2.0*numpy.pi)/sigma)*numpy.exp(-0.5*((frequencies-mu)/sigma)**2)
-        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._frequencyWindow))/dt)
+        self._omegaWindow = (numpy.sqrt(2.0*numpy.pi)/sigma)*numpy.exp(-0.5*((omegas-mu)/sigma)**2)
+        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._omegaWindow))/dt)

MDANSE/Framework/InstrumentResolutions/IInstrumentResolution.py

@@ -49,21 +49,21 @@ class IInstrumentResolution(Configurable):
         
         Configurable.__init__(self)
                         
-        self._frequencyWindow = None
+        self._omegaWindow = None
 
         self._timeWindow = None
         
     @abc.abstractmethod
-    def set_kernel(self, frequencies, dt):
+    def set_kernel(self, omegas, dt):
         pass    
     
     @property
-    def frequencyWindow(self):
+    def omegaWindow(self):
         
-        if self._frequencyWindow is None:
-            raise InstrumentResolutionError("Undefined frequency window")
+        if self._omegaWindow is None:
+            raise InstrumentResolutionError("Undefined omega window")
         
-        return self._frequencyWindow
+        return self._omegaWindow
 
     @property
     def timeWindow(self):

MDANSE/Framework/InstrumentResolutions/IdealResolution.py

@@ -44,9 +44,10 @@ class IdealInstrumentResolution(IInstrumentResolution):
     
     settings = collections.OrderedDict()
 
-    def set_kernel(self, frequencies, dt):
+    def set_kernel(self, omegas, dt):
                 
-        self._frequencyWindow = numpy.zeros(len(frequencies), dtype=numpy.float64)
-        self._frequencyWindow[len(frequencies)/2] = 1.0
+        nOmegas = len(omegas)
+        self._omegaWindow = numpy.zeros(nOmegas, dtype=numpy.float64)
+        self._omegaWindow[nOmegas/2] = 1.0
 
-        self._timeWindow = numpy.ones(len(frequencies), dtype=numpy.float64)
\ No newline at end of file
+        self._timeWindow = numpy.ones(nOmegas, dtype=numpy.float64)
\ No newline at end of file

MDANSE/Framework/InstrumentResolutions/LorentzianResolution.py

@@ -47,11 +47,11 @@ class LorentzianInstrumentResolution(IInstrumentResolution):
     settings['mu'] = ('float', {"default":0.0})
     settings['sigma'] = ('float', {"default":1.0})
 
-    def set_kernel(self, frequencies, dt):
+    def set_kernel(self, omegas, dt):
 
         mu = self._configuration["mu"]["value"]
         sigma = self._configuration["sigma"]["value"]
                                           
-        self._frequencyWindow = (2.0*sigma)/((frequencies-mu)**2 + sigma**2)
-        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._frequencyWindow))/dt)
+        self._omegaWindow = (2.0*sigma)/((omegas-mu)**2 + sigma**2)
+        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._omegaWindow))/dt)
                 
\ No newline at end of file

MDANSE/Framework/InstrumentResolutions/PseudoVoigtResolution.py

@@ -49,7 +49,7 @@ class PseudoVoigtInstrumentResolution(IInstrumentResolution):
     settings['mu_gaussian'] = ('float', {"default":0.0})
     settings['sigma_gaussian'] = ('float', {"default":1.0})
 
-    def set_kernel(self, frequencies, dt):
+    def set_kernel(self, omegas, dt):
 
         eta = self._configuration["eta"]["value"]
         muL = self._configuration["mu_lorentzian"]["value"]
@@ -57,10 +57,10 @@ class PseudoVoigtInstrumentResolution(IInstrumentResolution):
         muG = self._configuration["mu_gaussian"]["value"]
         sigmaG = self._configuration["sigma_gaussian"]["value"]
 
-        gaussian = (numpy.sqrt(2.0*numpy.pi)/sigmaG)*numpy.exp(-0.5*((frequencies-muG)/sigmaG)**2)
+        gaussian = (numpy.sqrt(2.0*numpy.pi)/sigmaG)*numpy.exp(-0.5*((omegas-muG)/sigmaG)**2)
                           
-        lorentzian = (2.0*sigmaL)/((frequencies-muL)**2 + sigmaL**2)
+        lorentzian = (2.0*sigmaL)/((omegas-muL)**2 + sigmaL**2)
         
-        self._frequencyWindow = eta*lorentzian + (1.0-eta)*gaussian
-        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._frequencyWindow))/dt)
+        self._omegaWindow = eta*lorentzian + (1.0-eta)*gaussian
+        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._omegaWindow))/dt)
                 
\ No newline at end of file

MDANSE/Framework/InstrumentResolutions/SquareResolution.py

@@ -46,12 +46,12 @@ class SquareInstrumentResolution(IInstrumentResolution):
     settings['mu'] = ('float', {"default":0.0})
     settings['sigma'] = ('float', {"default":1.0})
 
-    def set_kernel(self, frequencies, dt):
+    def set_kernel(self, omegas, dt):
                                 
         mu = self._configuration["mu"]["value"]
         sigma = self._configuration["sigma"]["value"]
                                 
-        self._frequencyWindow = 2.0*numpy.pi*numpy.where((numpy.abs(frequencies-mu)-sigma) > 0,0.0,1.0/(2.0*sigma))
+        self._omegaWindow = 2.0*numpy.pi*numpy.where((numpy.abs(omegas-mu)-sigma) > 0,0.0,1.0/(2.0*sigma))
                         
-        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._frequencyWindow))/dt)
+        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._omegaWindow))/dt)
         
\ No newline at end of file

MDANSE/Framework/InstrumentResolutions/TriangularResolution.py

@@ -46,13 +46,13 @@ class TriangularInstrumentResolution(IInstrumentResolution):
     settings['mu'] = ('float', {"default":0.0})
     settings['sigma'] = ('float', {"default":1.0})
 
-    def set_kernel(self, frequencies, dt):
+    def set_kernel(self, omegas, dt):
 
         mu = self._configuration["mu"]["value"]
         sigma = self._configuration["sigma"]["value"]
                                 
-        val = numpy.abs(frequencies-mu) - sigma
+        val = numpy.abs(omegas-mu) - sigma
                         
-        self._frequencyWindow = 2.0*numpy.pi*numpy.where( val >= 0, 0.0, -val/sigma**2)
+        self._omegaWindow = 2.0*numpy.pi*numpy.where( val >= 0, 0.0, -val/sigma**2)
         
-        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._frequencyWindow))/dt)
+        self._timeWindow = numpy.fft.fftshift(numpy.fft.ifft(numpy.fft.ifftshift(self._omegaWindow))/dt)

MDANSE/Framework/Jobs/AngularCorrelation.py

@@ -86,14 +86,14 @@ class AngularCorrelation(IJob):
                 
         self.numberOfSteps = self.configuration['axis_selection']['n_values']
 
-        self._outputData.add("times","line", self.configuration['frames']['time'],units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['time'],units='ps')
 
         self._outputData.add("axis_index","line", numpy.arange(self.configuration['axis_selection']['n_values']), units='au')
                         
-        self._outputData.add('ac',"line", (self.configuration['frames']['number'],), axis="times", units="au") 
+        self._outputData.add('ac',"line", (self.configuration['frames']['number'],), axis="time", units="au") 
 
         if self.configuration['per_axis']['value']:
-            self._outputData.add('ac_per_axis',"surface", (self.configuration['axis_selection']['n_values'],self.configuration['frames']['number'],), axis='axis_index|times', units="au") 
+            self._outputData.add('ac_per_axis',"surface", (self.configuration['axis_selection']['n_values'],self.configuration['frames']['number'],), axis='axis_index|time', units="au") 
 
     def run_step(self, index):
         """

MDANSE/Framework/Jobs/AreaPerMolecule.py

@@ -82,9 +82,9 @@ class AreaPerMolecule(IJob):
         if self._nMolecules == 0:
             raise AreaPerMoleculeError("No molecule matches %r name." % self.configuration["name"]["value"])
 
-        self._outputData.add("times", "line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time", "line", self.configuration['frames']['time'], units='ps')
 
-        self._outputData.add("area_per_molecule", "line", (self.configuration['frames']['number'],), axis="times", units="1/nm2")
+        self._outputData.add("area_per_molecule", "line", (self.configuration['frames']['number'],), axis="time", units="1/nm2")
                                          
     def run_step(self, index):
         """

MDANSE/Framework/Jobs/CurrentCorrelationFunction.py

@@ -82,13 +82,15 @@ class CurrentCorrelationFunction(IJob):
         
         self._instrResolution = self.configuration["instrument_resolution"]
         
-        self._nFrequencies = self._instrResolution['n_frequencies']
+        self._nOmegas = self._instrResolution['n_omegas']
                 
         self._outputData.add("q","line", numpy.array(self.configuration["q_vectors"]["shells"]), units="inv_nm") 
 
-        self._outputData.add("times","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time_window","line", self._instrResolution["time_window"], units="au") 
 
-        self._outputData.add("frequency","line", self._instrResolution["frequencies"],units='THz')
+        self._outputData.add("omega","line", self._instrResolution["omega"],units='rad/ps')
+        self._outputData.add("omega_window","line", self._instrResolution["omega_window"], axis="omega", units="au") 
 
         self._elements = self.configuration['atom_selection']['unique_names']
         self._elementsPairs = sorted(itertools.combinations_with_replacement(self._elements,2))
@@ -96,15 +98,15 @@ class CurrentCorrelationFunction(IJob):
         self._indexesPerElement = self.configuration['atom_selection'].get_indexes()
 
         for pair in self._elementsPairs:
-            self._outputData.add("j(q,t)_long_%s%s"  % pair,"surface", (nQShells,self._nFrames), axis="q|times", units="au")                                                 
-            self._outputData.add("j(q,t)_trans_%s%s" % pair,"surface", (nQShells,self._nFrames), axis="q|times", units="au")                                                 
-            self._outputData.add("J(q,f)_long_%s%s"  % pair,"surface", (nQShells,self._nFrequencies), axis="q|frequency", units="au") 
-            self._outputData.add("J(q,f)_trans_%s%s" % pair,"surface", (nQShells,self._nFrequencies), axis="q|frequency", units="au") 
-
-        self._outputData.add("j(q,t)_long_total","surface", (nQShells,self._nFrames), axis="q|times"    , units="au")                                                 
-        self._outputData.add("J(q,f)_long_total","surface", (nQShells,self._nFrequencies), axis="q|frequency", units="au") 
-        self._outputData.add("j(q,t)_trans_total","surface", (nQShells,self._nFrames), axis="q|times"    , units="au")                                                 
-        self._outputData.add("J(q,f)_trans_total","surface", (nQShells,self._nFrequencies), axis="q|frequency", units="au") 
+            self._outputData.add("j(q,t)_long_%s%s"  % pair,"surface", (nQShells,self._nFrames), axis="q|time", units="au")                                                 
+            self._outputData.add("j(q,t)_trans_%s%s" % pair,"surface", (nQShells,self._nFrames), axis="q|time", units="au")                                                 
+            self._outputData.add("J(q,f)_long_%s%s"  % pair,"surface", (nQShells,self._nOmegas), axis="q|omega", units="au") 
+            self._outputData.add("J(q,f)_trans_%s%s" % pair,"surface", (nQShells,self._nOmegas), axis="q|omega", units="au") 
+
+        self._outputData.add("j(q,t)_long_total","surface", (nQShells,self._nFrames), axis="q|time"    , units="au")                                                 
+        self._outputData.add("J(q,f)_long_total","surface", (nQShells,self._nOmegas), axis="q|omega", units="au") 
+        self._outputData.add("j(q,t)_trans_total","surface", (nQShells,self._nFrames), axis="q|time"    , units="au")                                                 
+        self._outputData.add("J(q,f)_trans_total","surface", (nQShells,self._nOmegas), axis="q|omega", units="au") 
          
     def run_step(self, index):
         """

MDANSE/Framework/Jobs/Density.py

@@ -67,11 +67,11 @@ class Density(IJob):
         self._symbols = sorted_atoms(self.configuration['trajectory']['instance'].universe,"symbol")
 
         # Will store the time.
-        self._outputData.add("times","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
 
-        self._outputData.add("mass_density","line", (self._nFrames,), units='g/cm3')
+        self._outputData.add("mass_density","line", (self._nFrames,), axis='time', units='g/cm3')
 
-        self._outputData.add("atomic_density","line", (self._nFrames,), units='1/cm3')
+        self._outputData.add("atomic_density","line", (self._nFrames,), axis='time', units='1/cm3')
 
         if not self.configuration['trajectory']['instance'].universe.is_periodic:
             raise JobError("Pair distribution function cannot be calculated for infinite universe trajectories")

MDANSE/Framework/Jobs/DensityOfStates.py

@@ -77,14 +77,14 @@ class DensityOfStates(IJob):
         self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
         self._outputData.add("time_window","line", instrResolution["time_window"], axis="time", units="au") 
 
-        self._outputData.add("frequency","line", instrResolution["frequencies"], units='THz')
-        self._outputData.add("frequency_window","line", instrResolution["frequency_window"], axis="frequency", units="au") 
+        self._outputData.add("omega","line", instrResolution["omega"], units='rad/ps')
+        self._outputData.add("omega_window","line", instrResolution["omega_window"], axis="omega", units="au") 
             
         for element in self.configuration['atom_selection']['unique_names']:
             self._outputData.add("vacf_%s" % element,"line", (self.configuration['frames']['number'],), axis="time", units="nm2/ps2") 
-            self._outputData.add("dos_%s" % element,"line", (instrResolution['n_frequencies'],), axis="frequency", units="nm2/ps") 
+            self._outputData.add("dos_%s" % element,"line", (instrResolution['n_omegas'],), axis="omega", units="nm2/ps") 
         self._outputData.add("vacf_total","line", (self.configuration['frames']['number'],), axis="time", units="nm2/ps2")         
-        self._outputData.add("dos_total","line", (instrResolution['n_frequencies'],), axis="frequency", units="nm2/ps")        
+        self._outputData.add("dos_total","line", (instrResolution['n_omegas'],), axis="omega", units="nm2/ps")        
         
     def run_step(self, index):
         """

MDANSE/Framework/Jobs/DensityProfile.py

@@ -148,7 +148,7 @@ class DensityProfile(IJob):
 
         dpTotal = weight(self.configuration["weights"].get_weights(),self._outputData,nAtomsPerElement,1,"dp_%s")
             
-        self._outputData.add("dp_total","line", dpTotal, axis="times", units="au") 
+        self._outputData.add("dp_total","line", dpTotal, axis="time", units="au") 
         
         self._extent /= self.numberOfSteps
                 

MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py

@@ -88,25 +88,25 @@ class DynamicCoherentStructureFactor(IJob):
         
         self._instrResolution = self.configuration["instrument_resolution"]
         
-        self._nFrequencies = self._instrResolution['n_frequencies']
+        self._nOmegas = self._instrResolution['n_omegas']
 
         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_window","line", self._instrResolution["time_window"], axis="time", units="au") 
+        self._outputData.add("time_window","line", self._instrResolution["time_window"], units="au") 
 
-        self._outputData.add("frequency","line", self._instrResolution["frequencies"], units='THz')
-        self._outputData.add("frequency_window","line", self._instrResolution["frequency_window"], axis="frequency", units="au") 
+        self._outputData.add("omega","line", self._instrResolution["omega"], units='rad/ps')
+        self._outputData.add("omega_window","line", self._instrResolution["omega_window"], axis="omega", units="au") 
                                 
         self._elementsPairs = sorted(itertools.combinations_with_replacement(self.configuration['atom_selection']['unique_names'],2))
         self._indexesPerElement = self.configuration['atom_selection'].get_indexes()
 
         for pair in self._elementsPairs:
-            self._outputData.add("f(q,t)_%s%s" % pair,"surface", (nQShells,self._nFrames),axis="q|time"     , units="au")                                                 
-            self._outputData.add("s(q,f)_%s%s" % pair,"surface", (nQShells,self._nFrequencies), axis="q|frequency", units="nm2/ps") 
+            self._outputData.add("f(q,t)_%s%s" % pair,"surface", (nQShells,self._nFrames),axis="q|time", units="au")                                                 
+            self._outputData.add("s(q,f)_%s%s" % pair,"surface", (nQShells,self._nOmegas), axis="q|omega", units="nm2/ps") 
 
         self._outputData.add("f(q,t)_total","surface", (nQShells,self._nFrames), axis="q|time", units="au")                                                 
-        self._outputData.add("s(q,f)_total","surface", (nQShells,self._nFrequencies), axis="q|frequency", units="nm2/ps") 
+        self._outputData.add("s(q,f)_total","surface", (nQShells,self._nOmegas), axis="q|omega", units="nm2/ps") 
  
     def run_step(self, index):
         """
@@ -176,7 +176,7 @@ class DynamicCoherentStructureFactor(IJob):
             self._outputData["s(q,f)_%s%s" % pair][:] = get_spectrum(self._outputData["f(q,t)_%s%s" % pair],
                                                                      self.configuration["instrument_resolution"]["time_window"],
                                                                      self.configuration["instrument_resolution"]["time_step"],
-                                                                     axis=1)        
+                                                                     axis=1)
         
         fqtTotal = weight(self.configuration["weights"].get_weights(),self._outputData,nAtomsPerElement,2,"f(q,t)_%s%s")
 

MDANSE/Framework/Jobs/DynamicIncoherentStructureFactor.py

@@ -79,22 +79,22 @@ class DynamicIncoherentStructureFactor(IJob):
         
         self._instrResolution = self.configuration["instrument_resolution"]
         
-        self._nFrequencies = self._instrResolution['n_frequencies']
+        self._nOmegas = self._instrResolution['n_omegas']
 
         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_window","line", self._instrResolution["time_window"], axis="time", units="au") 
 
-        self._outputData.add("frequency","line", self._instrResolution["frequencies"], units='THz')
-        self._outputData.add("frequency_window","line", self._instrResolution["frequency_window"], axis="frequency", units="au") 
+        self._outputData.add("omega","line", self._instrResolution["omega"], units='rad/ps')
+        self._outputData.add("omega_window","line", self._instrResolution["omega_window"], axis="omega", units="au") 
                         
         for element in self.configuration['atom_selection']['unique_names']:
             self._outputData.add("f(q,t)_%s" % element,"surface", (self._nQShells,self._nFrames)     , axis="q|time", units="au")                                                 
-            self._outputData.add("s(q,f)_%s" % element,"surface", (self._nQShells,self._nFrequencies), axis="q|frequency", units="nm2/ps") 
+            self._outputData.add("s(q,f)_%s" % element,"surface", (self._nQShells,self._nOmegas), axis="q|omega", units="nm2/ps") 
 
         self._outputData.add("f(q,t)_total","surface", (self._nQShells,self._nFrames)     , axis="q|time", units="au")                                                 
-        self._outputData.add("s(q,f)_total","surface", (self._nQShells,self._nFrequencies), axis="q|frequency", units="nm2/ps") 
+        self._outputData.add("s(q,f)_total","surface", (self._nQShells,self._nOmegas), axis="q|omega", units="nm2/ps") 
     
     def run_step(self, index):
         """

MDANSE/Framework/Jobs/GaussianDynamicIncoherentStructureFactor.py

@@ -79,7 +79,7 @@ class GaussianDynamicIncoherentStructureFactor(IJob):
         
         self._instrResolution = self.configuration["instrument_resolution"]
         
-        self._nFrequencies = self._instrResolution['n_frequencies']
+        self._nOmegas = self._instrResolution['n_omegas']
         
         self._kSquare = self.configuration["q_shells"]["value"]**2
         
@@ -87,18 +87,18 @@ class GaussianDynamicIncoherentStructureFactor(IJob):
 
         self._outputData.add("q2","line",self._kSquare,units="inv_nm**2") 
 
-        self._outputData.add("times","line",self.configuration['frames']['time'], units='ps')
-        self._outputData.add("time_window","line",self._instrResolution["time_window"], axis="times", units="au") 
+        self._outputData.add("time","line",self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time_window","line",self._instrResolution["time_window"], axis="time", units="au") 
 
-        self._outputData.add("frequency","line",self.configuration["instrument_resolution"]["frequencies"], units='THz')
-        self._outputData.add("frequency_window","line",self._instrResolution["frequency_window"], axis="frequency", units="au") 
+        self._outputData.add("omega","line",self.configuration["instrument_resolution"]["omega"], units='rad/ps')
+        self._outputData.add("omega_window","line",self._instrResolution["omega_window"], axis="omega", units="au") 
 
         for element in self.configuration['atom_selection']['unique_names']:
-            self._outputData.add("f(q,t)_%s" % element,"surface", (self._nQShells,self._nFrames),axis="q|times", units="au")                                                 
-            self._outputData.add("s(q,f)_%s" % element,"surface", (self._nQShells,self._nFrequencies), axis="q|frequency", units="nm2/ps") 
+            self._outputData.add("f(q,t)_%s" % element,"surface", (self._nQShells,self._nFrames),axis="q|time", units="au")                                                 
+            self._outputData.add("s(q,f)_%s" % element,"surface", (self._nQShells,self._nOmegas), axis="q|omega", units="nm2/ps") 
 
-        self._outputData.add("f(q,t)_total","surface",(self._nQShells,self._nFrames), axis="q|times", units="au")                                                 
-        self._outputData.add("s(q,f)_total","surface",(self._nQShells,self._nFrequencies), axis="q|frequency", units="nm2/ps") 
+        self._outputData.add("f(q,t)_total","surface",(self._nQShells,self._nFrames), axis="q|time", units="au")                                                 
+        self._outputData.add("s(q,f)_total","surface",(self._nQShells,self._nOmegas), axis="q|omega", units="nm2/ps") 
         
     def run_step(self, index):
         """

MDANSE/Framework/Jobs/IJob.py

@@ -515,7 +515,7 @@ class %s(IJob):
         self.numberOfSteps = self.configuration['frames']['number']
                         
         # Create an output data for the selected frames.
-        self._outputData.add("times", "line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time", "line", self.configuration['frames']['time'], units='ps')
 
 
     def run_step(self, index):

MDANSE/Framework/Jobs/McStasVirtualInstrument.py

@@ -79,11 +79,11 @@ class McStasVirtualInstrument(IJob):
     settings['frames'] = ('frames', {"dependencies":{'trajectory':'trajectory'}})
     settings['sample_coh'] = ('netcdf_input_file', {"widget":'input_file',
                                                     "label":'MDANSE Coherent Structure Factor',
-                                                    "variables":['q','frequency','s(q,f)_total'],
+                                                    "variables":['q','omega','s(q,f)_total'],
                                                     'default' : os.path.join('..','..','..','Data','NetCDF','dcsf_prot.nc')})
     settings['sample_inc'] = ('netcdf_input_file', {"widget":'input_file',
                                                     "label":'MDANSE Incoherent Structure Factor',
-                                                    "variables" :['q','frequency','s(q,f)_total'],
+                                                    "variables" :['q','omega','s(q,f)_total'],
                                                     'default':os.path.join('..','..','..','Data','NetCDF','disf_prot.nc')})
     settings['temperature'] = ('float', {"default":298.0})
     settings['display'] = ('boolean', {'label':'trace the 3D view of the simulation'})

MDANSE/Framework/Jobs/MeanSquareDisplacement.py

@@ -90,11 +90,11 @@ class MeanSquareDisplacement(IJob):
         self.numberOfSteps = self.configuration['atom_selection']['selection_length']
                         
         # Will store the time.
-        self._outputData.add("times", "line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time", "line", self.configuration['frames']['time'], units='ps')
                         
         # Will store the mean square displacement evolution.
         for element in self.configuration['atom_selection']['unique_names']:
-            self._outputData.add("msd_%s" % element, "line", (self.configuration['frames']['number'],), axis="times", units="nm2") 
+            self._outputData.add("msd_%s" % element, "line", (self.configuration['frames']['number'],), axis="time", units="nm2") 
 
     def run_step(self, index):
         """
@@ -152,7 +152,7 @@ class MeanSquareDisplacement(IJob):
         weights = self.configuration["weights"].get_weights()
         msdTotal = weight(weights,self._outputData,nAtomsPerElement,1,"msd_%s")
         
-        self._outputData.add("msd_total", "line", msdTotal, axis="times", units="nm2") 
+        self._outputData.add("msd_total", "line", msdTotal, axis="time", units="nm2") 
         
         self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)
         

MDANSE/Framework/Jobs/OrderParameter.py

@@ -100,7 +100,7 @@ class OrderParameter(IJob):
         
         self.numberOfSteps = self._nAxis
 
-        self._outputData.add("times","line", self.configuration['frames']['time'], units='ps')
+        self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
 
         self._outputData.add("axis_index","line", numpy.arange(self.configuration['axis_selection']['n_values']), units='au')
                         
@@ -117,13 +117,13 @@ class OrderParameter(IJob):
         else:
             self._doRotation = True
 
-        self._outputData.add('p1',"line", (self._nFrames,), axis='times', units="au") 
-        self._outputData.add('p2',"line", (self._nFrames,), axis='times', units="au") 
-        self._outputData.add('s2',"line", (self._nAxis,), axis='times', units="au") 
+        self._outputData.add('p1',"line", (self._nFrames,), axis='time', units="au") 
+        self._outputData.add('p2',"line", (self._nFrames,), axis='time', units="au") 
+        self._outputData.add('s2',"line", (self._nAxis,), axis='time', units="au") 
             
         if self.configuration['per_axis']['value']:
-            self._outputData.add('p1_per_axis',"surface", (self._nAxis,self._nFrames), axis='axis_index|times', units="au") 
-            self._outputData.add('p2_per_axis',"surface", (self._nAxis,self._nFrames), axis='axis_index|times', units="au") 
+            self._outputData.add('p1_per_axis',"surface", (self._nAxis,self._nFrames), axis='axis_index|time', units="au") 
+            self._outputData.add('p2_per_axis',"surface", (self._nAxis,self._nFrames), axis='axis_index|time', units="au") 
 
     def run_step(self, index):
         """

MDANSE/Framework/Jobs/StructureFactorFromScatteringFunction.py

@@ -73,18 +73,18 @@ class StructureFactorFromScatteringFunction(IJob):
 
         self._outputData.add("q","line", inputFile.variables['q'].getValue(), units="inv_nm") 
 
-        self._outputData.add("frequency","line", resolution["frequencies"], units='THz')
+        self._outputData.add("omega","line", resolution["omega"], units='rad/ps')
         
-        self._outputData.add("frequency_window","line", resolution["frequency_window"], axis="frequency", units="au") 
+        self._outputData.add("omega_window","line", resolution["omega_window"], axis="omega", units="au") 
 
         nQVectors = len(inputFile.variables['q'].getValue())
-        nFrequencies = resolution['n_frequencies']
+        nOmegas = resolution['n_omegas']
 
         for k, v in inputFile.variables.items():
             if k.startswith('f(q,t)_'):
                 self._outputData.add(k,"surface", v.getValue(), axis="q|time", units="au")