Improve DISF+DCSF summation

MDANSE/Src/MDANSE/Core/Platform.py

@@ -45,11 +45,11 @@ def __new__(cls, *args, **kwargs):
         """
         Create a new instance of Platform class.
 
-        :param cls: the class to instanciate.
+        :param cls: the class to instantiate.
         :type cls: class
         """
 
-        # Case of the first instanciation.
+        # Case of the first instantiation.
         if cls.__instance is None:
             cls.__instance = super(Platform, cls).__new__(cls, *args, **kwargs)
 

MDANSE/Src/MDANSE/Core/Singleton.py

@@ -24,7 +24,7 @@ class Singleton(type):
 
     def __call__(self, *args, **kwargs):
         """
-        Creates (or returns if it has already been instanciated) an instance of the class.
+        Creates (or returns if it has already been instantiated) an instance of the class.
         """
 
         if self.__name__ not in self.__instances:

MDANSE/Src/MDANSE/Framework/Configurators/WeightsConfigurator.py

@@ -106,20 +106,24 @@ def configure(self, value):
         self.error_status = "OK"
 
     def get_weights(self):
-        ascfg = self._configurable[self._dependencies["atom_selection"]]
+        atom_selection_configurator = self._configurable[
+            self._dependencies["atom_selection"]
+        ]
 
         weights = {}
-        for i in range(ascfg["selection_length"]):
-            name = ascfg["names"][i]
-            for el in ascfg["elements"][i]:
-                p = ATOMS_DATABASE.get_atom_property(el, self["property"])
+        for i in range(atom_selection_configurator["selection_length"]):
+            name = atom_selection_configurator["names"][i]
+            for element in atom_selection_configurator["elements"][i]:
+                property = ATOMS_DATABASE.get_atom_property(element, self["property"])
                 if name in weights:
-                    weights[name] += p
+                    weights[name] += property
                 else:
-                    weights[name] = p
+                    weights[name] = property
 
-        for k, v in list(ascfg.get_natoms().items()):
-            weights[k] /= v
+        for element, num_atoms in list(
+            atom_selection_configurator.get_natoms().items()
+        ):
+            weights[element] /= num_atoms
 
         return weights
 

MDANSE/Src/MDANSE/Framework/Jobs/CurrentCorrelationFunction.py

@@ -21,7 +21,7 @@
 from scipy.signal import correlate
 
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 from MDANSE.Mathematics.Signal import (
     differentiate,
     get_spectrum,
@@ -391,36 +391,34 @@ def finalize(self):
                 fft="rfft",
             )
 
-        jqtLongTotal = weight(
-            self.configuration["weights"].get_weights(),
+        weights = self.configuration["weights"].get_weights()
+        weight_dict = get_weights(weights, nAtomsPerElement, 2)
+        assign_weights(self._outputData, weight_dict, "j(q,t)_long_%s%s")
+        assign_weights(self._outputData, weight_dict, "j(q,t)_trans_%s%s")
+        assign_weights(self._outputData, weight_dict, "J(q,f)_long_%s%s")
+        assign_weights(self._outputData, weight_dict, "J(q,f)_trans_%s%s")
+        jqtLongTotal = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            2,
+            weight_dict,
             "j(q,t)_long_%s%s",
         )
         self._outputData["j(q,t)_long_total"][:] = jqtLongTotal
-        jqtTransTotal = weight(
-            self.configuration["weights"].get_weights(),
+        jqtTransTotal = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            2,
+            weight_dict,
             "j(q,t)_trans_%s%s",
         )
         self._outputData["j(q,t)_trans_total"][:] = jqtTransTotal
 
-        sqfLongTotal = weight(
-            self.configuration["weights"].get_weights(),
+        sqfLongTotal = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            2,
+            weight_dict,
             "J(q,f)_long_%s%s",
         )
         self._outputData["J(q,f)_long_total"][:] = sqfLongTotal
-        sqfTransTotal = weight(
-            self.configuration["weights"].get_weights(),
+        sqfTransTotal = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            2,
+            weight_dict,
             "J(q,f)_trans_%s%s",
         )
         self._outputData["J(q,f)_trans_total"][:] = sqfTransTotal

MDANSE/Src/MDANSE/Framework/Jobs/DensityOfStates.py

@@ -18,7 +18,7 @@
 from scipy.signal import correlate
 
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 from MDANSE.Mathematics.Signal import differentiate, get_spectrum
 from MDANSE.MolecularDynamics.TrajectoryUtils import sorted_atoms
 from MDANSE.MLogging import LOG
@@ -238,21 +238,20 @@ def finalize(self):
             )
 
         weights = self.configuration["weights"].get_weights()
-        self._outputData["vacf_total"][:] = weight(
-            weights,
+        weight_dict = get_weights(weights, nAtomsPerElement, 1)
+        assign_weights(self._outputData, weight_dict, "vacf_%s")
+        assign_weights(self._outputData, weight_dict, "dos_%s")
+        self._outputData["vacf_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            1,
+            weight_dict,
             "vacf_%s",
-            update_partials=True,
+            update_partials=False,
         )
-        self._outputData["dos_total"][:] = weight(
-            weights,
+        self._outputData["dos_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            1,
+            weight_dict,
             "dos_%s",
-            update_partials=True,
+            update_partials=False,
         )
 
         self._outputData.write(

MDANSE/Src/MDANSE/Framework/Jobs/DensityProfile.py

@@ -21,7 +21,7 @@
 
 from MDANSE.Core.Error import Error
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 
 
 class DensityProfileError(Error):
@@ -176,11 +176,12 @@ def finalize(self):
         for element in n_atoms_per_element.keys():
             self._outputData["dp_%s" % element] += self.numberOfSteps
 
-        dp_total = weight(
-            self.configuration["weights"].get_weights(),
+        weights = self.configuration["weights"].get_weights()
+        weight_dict = get_weights(weights, n_atoms_per_element, 1)
+        assign_weights(self._outputData, weight_dict, "dp_%s")
+        dp_total = weighted_sum(
             self._outputData,
-            n_atoms_per_element,
-            1,
+            weight_dict,
             "dp_%s",
         )
 

MDANSE/Src/MDANSE/Framework/Jobs/DynamicCoherentStructureFactor.py

@@ -22,7 +22,7 @@
 
 from MDANSE.Core.Error import Error
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 from MDANSE.Mathematics.Signal import get_spectrum
 
 
@@ -249,33 +249,36 @@ def finalize(self):
         """
 
         nAtomsPerElement = self.configuration["atom_selection"].get_natoms()
+
+        weights = self.configuration["weights"].get_weights()
+        weight_dict = get_weights(weights, nAtomsPerElement, 2)
+        assign_weights(self._outputData, weight_dict, "f(q,t)_%s%s")
+        assign_weights(self._outputData, weight_dict, "s(q,f)_%s%s")
         for pair in self._elementsPairs:
             ni = nAtomsPerElement[pair[0]]
             nj = nAtomsPerElement[pair[1]]
-            self._outputData["f(q,t)_%s%s" % pair][:] /= np.sqrt(ni * nj)
+            extra_scaling = 1.0 / np.sqrt(ni * nj)
+            self._outputData["f(q,t)_%s%s" % pair].scaling_factor *= extra_scaling
             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,
             )
+            self._outputData["s(q,f)_%s%s" % pair].scaling_factor *= extra_scaling
 
-        self._outputData["f(q,t)_total"][:] = weight(
-            self.configuration["weights"].get_weights(),
+        self._outputData["f(q,t)_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            2,
+            weight_dict,
             "f(q,t)_%s%s",
-            update_partials=True,
+            update_partials=False,
         )
 
-        self._outputData["s(q,f)_total"][:] = weight(
-            self.configuration["weights"].get_weights(),
+        self._outputData["s(q,f)_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            2,
+            weight_dict,
             "s(q,f)_%s%s",
-            update_partials=True,
+            update_partials=False,
         )
 
         self._outputData.write(

MDANSE/Src/MDANSE/Framework/Jobs/DynamicIncoherentStructureFactor.py

@@ -20,7 +20,7 @@
 from scipy.signal import correlate
 
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 from MDANSE.Mathematics.Signal import get_spectrum
 from MDANSE.MolecularDynamics.TrajectoryUtils import sorted_atoms
 
@@ -255,33 +255,33 @@ def finalize(self):
         """
 
         nAtomsPerElement = self.configuration["atom_selection"].get_natoms()
+        weights = self.configuration["weights"].get_weights()
+        weight_dict = get_weights(weights, nAtomsPerElement, 1)
+        assign_weights(self._outputData, weight_dict, "f(q,t)_%s")
+        assign_weights(self._outputData, weight_dict, "s(q,f)_%s")
         for element, number in list(nAtomsPerElement.items()):
-            self._outputData["f(q,t)_%s" % element][:] /= number
+            extra_scaling = 1.0 / number
+            self._outputData["f(q,t)_%s" % element].scaling_factor *= extra_scaling
             self._outputData["s(q,f)_%s" % element][:] = get_spectrum(
                 self._outputData["f(q,t)_%s" % element],
                 self.configuration["instrument_resolution"]["time_window"],
                 self.configuration["instrument_resolution"]["time_step"],
                 axis=1,
             )
+            self._outputData["s(q,f)_%s" % element].scaling_factor *= extra_scaling
 
-        weights = self.configuration["weights"].get_weights()
-
-        self._outputData["f(q,t)_total"][:] = weight(
-            weights,
+        self._outputData["f(q,t)_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            1,
+            weight_dict,
             "f(q,t)_%s",
-            update_partials=True,
+            update_partials=False,
         )
 
-        self._outputData["s(q,f)_total"][:] = weight(
-            weights,
+        self._outputData["s(q,f)_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            1,
+            weight_dict,
             "s(q,f)_%s",
-            update_partials=True,
+            update_partials=False,
         )
 
         self._outputData.write(

MDANSE/Src/MDANSE/Framework/Jobs/ElasticIncoherentStructureFactor.py

@@ -19,7 +19,7 @@
 import numpy as np
 
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 from MDANSE.MolecularDynamics.TrajectoryUtils import sorted_atoms
 
 
@@ -198,13 +198,13 @@ def finalize(self):
             self._outputData["eisf_%s" % element][:] /= number
 
         weights = self.configuration["weights"].get_weights()
-        self._outputData["eisf_total"][:] = weight(
-            weights,
+        weight_dict = get_weights(weights, nAtomsPerElement, 1)
+        assign_weights(self._outputData, weight_dict, "eisf_%s")
+        self._outputData["eisf_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            1,
+            weight_dict,
             "eisf_%s",
-            update_partials=True,
+            update_partials=False,
         )
 
         self._outputData.write(

MDANSE/Src/MDANSE/Framework/Jobs/GaussianDynamicIncoherentStructureFactor.py

@@ -19,7 +19,7 @@
 import numpy as np
 
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 from MDANSE.Mathematics.Signal import get_spectrum
 from MDANSE.MolecularDynamics.Analysis import mean_square_displacement
 from MDANSE.MolecularDynamics.TrajectoryUtils import sorted_atoms
@@ -250,23 +250,21 @@ def finalize(self):
                 axis=1,
             )
         weights = self.configuration["weights"].get_weights()
-
-        self._outputData["f(q,t)_total"][:] = weight(
-            weights,
+        weight_dict = get_weights(weights, nAtomsPerElement, 1)
+        assign_weights(self._outputData, weight_dict, "f(q,t)_%s")
+        assign_weights(self._outputData, weight_dict, "s(q,f)_%s")
+        self._outputData["f(q,t)_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            1,
+            weight_dict,
             "f(q,t)_%s",
-            update_partials=True,
+            update_partials=False,
         )
 
-        self._outputData["s(q,f)_total"][:] = weight(
-            weights,
+        self._outputData["s(q,f)_total"][:] = weighted_sum(
             self._outputData,
-            nAtomsPerElement,
-            1,
+            weight_dict,
             "s(q,f)_%s",
-            update_partials=True,
+            update_partials=False,
         )
 
         self._outputData.write(

MDANSE/Src/MDANSE/Framework/Jobs/GeneralAutoCorrelationFunction.py

@@ -17,7 +17,7 @@
 import collections
 
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Mathematics.Arithmetic import weight
+from MDANSE.Mathematics.Arithmetic import assign_weights, get_weights, weighted_sum
 from MDANSE.Mathematics.Signal import correlation, normalize
 
 
@@ -163,12 +163,14 @@ def finalize(self):
                 if self._outputData["gacf_{}}".format(element)][0] == 0:
                     raise ValueError("The normalization factor is equal to zero")
                 else:
-                    self._outputData["gacf_{}".format(element)] = normalize(
+                    self._outputData["gacf_{}".format(element)][:] = normalize(
                         self._outputData["gacf_%s" % element], axis=0
                     )
 
         weights = self.configuration["weights"].get_weights()
-        gacfTotal = weight(weights, self._outputData, nAtomsPerElement, 1, "gacf_%s")
+        weight_dict = get_weights(weights, nAtomsPerElement, 1)
+        assign_weights(self._outputData, weight_dict, "gacf_%s")
+        gacfTotal = weighted_sum(self._outputData, weight_dict, "gacf_%s")
 
         self._outputData["gacf_total"][:] = gacfTotal