Merge pull request #388 from ISISNeutronMuon/chi/fold-change

Coordinate folding change
ISISNeutronMuon · Mar 25, 2024 · 87de379 · 87de379
2 parents 789e6d5 + bbdc4f6
commit 87de379
Show file tree

Hide file tree

Showing 6 changed files with 23 additions and 12 deletions.
diff --git a/MDANSE/Extensions/fold_coordinates.pyx b/MDANSE/Extensions/fold_coordinates.pyx
@@ -76,22 +76,22 @@ def fold_coordinates(
             by = box_coords[i,j,1]
             bz = box_coords[i,j,2]
 
-            while bx < -0.5:
+            while bx < 0.0:
                 bx += 1.0
 
-            while by < -0.5:
+            while by < 0.0:
                 by += 1.0
 
-            while bz < -0.5:
+            while bz < 0.0:
                 bz += 1.0
 
-            while bx > 0.5:
+            while bx >= 1.0:
                 bx -= 1.0
 
-            while by > 0.5:
+            while by >= 1.0:
                 by -= 1.0
 
-            while bz > 0.5:
+            while bz >= 1.0:
                 bz -= 1.0
 
             box_coords[i,j,0] = bx

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/ASE.py b/MDANSE/Src/MDANSE/Framework/Converters/ASE.py
@@ -79,6 +79,10 @@ class ASE(Converter):
             "mini": 0,
         },
     )
+    settings["fold"] = (
+        "BooleanConfigurator",
+        {"default": False, "label": "Fold coordinates into box"},
+    )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",
         {
@@ -156,6 +160,8 @@ def run_step(self, index):
             realConf = PeriodicRealConfiguration(
                 self._trajectory.chemical_system, coords, unitCell
             )
+            if self._configuration["fold"]["value"]:
+                realConf.fold_coordinates()
         else:
             realConf = RealConfiguration(
                 self._trajectory.chemical_system,

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py b/MDANSE/Src/MDANSE/Framework/Converters/CP2K.py
@@ -140,6 +140,10 @@ class CP2K(Converter):
             "dependencies": {"input_file": "pos_file"},
         },
     )
+    settings["fold"] = (
+        "BooleanConfigurator",
+        {"default": False, "label": "Fold coordinates into box"},
+    )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",
         {
@@ -232,7 +236,8 @@ def run_step(self, index):
             self._trajectory.chemical_system, coords, unitcell, **variables
         )
 
-        realConf.fold_coordinates()
+        if self._configuration["fold"]["value"]:
+            realConf.fold_coordinates()
 
         self._trajectory.chemical_system.configuration = realConf
 

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/DFTB.py b/MDANSE/Src/MDANSE/Framework/Converters/DFTB.py
@@ -54,7 +54,7 @@ class DFTB(Forcite):
     )
     settings["fold"] = (
         "BooleanConfigurator",
-        {"default": True, "label": "Fold coordinates in to box"},
+        {"default": False, "label": "Fold coordinates into box"},
     )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",

diff --git a/MDANSE/Src/MDANSE/Framework/Converters/Discover.py b/MDANSE/Src/MDANSE/Framework/Converters/Discover.py
@@ -275,7 +275,7 @@ class Discover(Converter):
     )
     settings["fold"] = (
         "BooleanConfigurator",
-        {"default": True, "label": "Fold coordinates into box"},
+        {"default": False, "label": "Fold coordinates into box"},
     )
     settings["output_file"] = (
         "OutputTrajectoryConfigurator",

diff --git a/MDANSE/Tests/UnitTests/test_configuration.py b/MDANSE/Tests/UnitTests/test_configuration.py
@@ -449,9 +449,9 @@ def test_fold_coordinates(self):
             np.allclose(
                 conf["coordinates"],
                 [
-                    [-0.65955991, 1.40648987, -1.9977125],
-                    [1.04665145, -1.06488218, -0.1532281],
-                    [-0.27479577, -0.08878546, 1.93534948],
+                    [1.34044009, 2.40648987, -1.9977125],
+                    [0.04665145, 1.93511782, -0.1532281],
+                    [1.72520423, 0.91121454, -2.06465052],
                     [-0.22366532, 1.38389029, -0.29560999],
                 ],
                 rtol=1.0e-6,