Enforce copy-on-set for md

pnnl · Aug 17, 2023 · d718fb6 · d718fb6
1 parent 6dec1dd
commit d718fb6
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/isicle/geometry.py b/isicle/geometry.py
@@ -106,7 +106,7 @@ def md(self, program="xtb", **kwargs):
 
         """
 
-        return isicle.md.md(self.__copy__(), program=program, **kwargs)
+        return isicle.md.md(self, program=program, **kwargs)
 
     def ionize(self, ion_path=None, ion_list=None, **kwargs):
         """

diff --git a/isicle/md.py b/isicle/md.py
@@ -106,7 +106,7 @@ def set_geometry(self, geom):
         """
 
         # Assign geometry
-        self.geom = geom
+        self.geom = geom.__copy__()
         self.basename = self.geom.basename
 
         # Save geometry
@@ -426,7 +426,9 @@ def run(self, geom, task='optimize', forcefield='gfn2', charge=None,
         self.set_geometry(geom)
 
         # Configure
-        self.configure(**kwargs)
+        self.configure(task=task, forcefield=forcefield, charge=charge,
+            ewin=ewin, ion=ion, optlevel=optlevel, dryrun=dryrun, processes=processes,
+            solvation=solvation, ignore_topology=ignore_topology)
 
         # Run QM simulation
         self.submit()
@@ -716,7 +718,7 @@ def set_geometry(self, geom):
         """
 
         # Assign geometry
-        self.geom = geom
+        self.geom = geom.__copy__()
         self.basename = self.geom.basename
 
         self.tinkerxyz = self._convert_to_tinkerxyz()