Merge pull request #28 from molssi-seamm/dev

Switching periodic systems to fractional coordinates.
molssi-seamm · Sep 6, 2023 · 3b67f46 · 3b67f46
2 parents d30d645 + f7b3be2
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diff --git a/HISTORY.rst b/HISTORY.rst
@@ -2,6 +2,12 @@
 History
 =======
 
+2023.9.6 -- Using fractional coordinates for periodic systems.
+    * By convention, SEAMM is using fractional coordinates for periodic systems. The
+      PACKMOL step was creating periodic structures with Cartesian coordinates, which
+      can be a bit confusing, though it did not affect any reauls. This change fixes the
+      issue. 
+
 2023.2.15 -- Restructured documentation and moved to new theme.
 
 2022.5.31 -- Substantial enhancements

diff --git a/packmol_step/packmol.py b/packmol_step/packmol.py
@@ -296,6 +296,10 @@ def run(self):
             configuration.periodicity = 3
             a, b, c = cell
             configuration.cell.parameters = (a, b, c, 90.0, 90.0, 90.0)
+            # by convention we keep periodic systems in fractional coordinates
+            xyz = configuration.atoms.get_coordinates(fractionals=False)
+            configuration.coordinate_system = "fractional"
+            configuration.atoms.set_coordinates(xyz, fractionals=False)
 
         printer.important(__(output, indent=4 * " "))
         printer.important("")