Improve default input parameters of DistanceHistogram-based jobs

ISISNeutronMuon · Jan 24, 2025 · 3407469 · 3407469
1 parent b3bb2ec
commit 3407469
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Showing 3 changed files with 25 additions and 8 deletions.
diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/CoordinationNumber.py b/MDANSE/Src/MDANSE/Framework/Jobs/CoordinationNumber.py
@@ -46,8 +46,14 @@ class CoordinationNumber(DistanceHistogram):
         {"dependencies": {"trajectory": "trajectory"}},
     )
     settings["r_values"] = (
-        "RangeConfigurator",
-        {"valueType": float, "includeLast": True, "mini": 0.0},
+        "DistHistCutoffConfigurator",
+        {
+            "label": "r values (nm)",
+            "valueType": float,
+            "includeLast": True,
+            "mini": 0.0,
+            "dependencies": {"trajectory": "trajectory"},
+        },
     )
     settings["atom_selection"] = (
         "AtomSelectionConfigurator",
@@ -159,7 +165,7 @@ def finalize(self):
                 self.hIntra[idi, idj] += self.hIntra[idj, idi]
                 self.hInter[idi, idj] += self.hInter[idj, idi]
 
-            fact = nij * nFrames * shellVolumes
+            fact = 2 * nij * nFrames * shellVolumes
 
             self.hIntra[idi, idj, :] /= fact
             self.hInter[idi, idj, :] /= fact

diff --git a/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py b/MDANSE/Src/MDANSE/Framework/Jobs/XRayStaticStructureFactor.py
@@ -68,12 +68,18 @@ class XRayStaticStructureFactor(DistanceHistogram):
         {"dependencies": {"trajectory": "trajectory"}},
     )
     settings["r_values"] = (
-        "RangeConfigurator",
-        {"valueType": float, "includeLast": True, "mini": 0.0},
+        "DistHistCutoffConfigurator",
+        {
+            "label": "r values (nm)",
+            "valueType": float,
+            "includeLast": True,
+            "mini": 0.0,
+            "dependencies": {"trajectory": "trajectory"},
+        },
     )
     settings["q_values"] = (
         "RangeConfigurator",
-        {"valueType": float, "includeLast": True, "mini": 0.0},
+        {"valueType": float, "includeLast": True, "mini": 0.0, "default": (0, 500, 1)},
     )
     settings["atom_selection"] = (
         "AtomSelectionConfigurator",
@@ -164,7 +170,7 @@ def finalize(self):
                 self.hIntra[idi, idj] += self.hIntra[idj, idi]
                 self.hInter[idi, idj] += self.hInter[idj, idi]
 
-            fact = nij * nFrames * shellVolumes
+            fact = 2 * nij * nFrames * shellVolumes
 
             pdfIntra = self.hIntra[idi, idj, :] / fact
             pdfInter = self.hInter[idi, idj, :] / fact

diff --git a/MDANSE/Src/MDANSE/Mathematics/Arithmetic.py b/MDANSE/Src/MDANSE/Mathematics/Arithmetic.py
@@ -37,7 +37,12 @@ def get_weights(props, contents, dim):
         else:
             normFactor += fact
 
-    if abs(normFactor) > 0.0:  # if normFactor is 0, all weights are 0 too.
+    normalise = True
+    try:
+        len(normFactor)
+    except TypeError:
+        normalise = abs(normFactor) > 0.0  # if normFactor is 0, all weights are 0 too.
+    if normalise:
         for k in list(weights.keys()):
             weights[k] /= np.float64(normFactor)