Ensure we store which atoms are fixed

exalearn · Oct 25, 2023 · 9ee633a · 9ee633a
1 parent 49dfcff
commit 9ee633a
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/examol/simulate/base.py b/examol/simulate/base.py
@@ -38,7 +38,7 @@ def __post_init__(self):
             self.xyz = write_to_string(atoms, 'xyz')
         else:
             atoms.calc = None
-            self.xyz = write_to_string(atoms, 'extxyz')
+            self.xyz = write_to_string(atoms, 'extxyz', columns=['symbols', 'positions', 'move_mask'])
 
     @property
     def atoms(self) -> ase.Atoms:

diff --git a/examol/store/recipes/surface.py b/examol/store/recipes/surface.py
@@ -43,7 +43,7 @@ class SurfaceSite:
 
 @dataclass()
 class SurfaceRecord:
-    """Describe the surface on which molecule are Adsorbed"""
+    """Describe the surface on which molecule are adsorbed"""
 
     # Definition of the cell
     name: str = ...
@@ -65,8 +65,9 @@ class AdsorptionEnergy(PropertyRecipe):
     Each file contains the relaxed geometry of the slab, and information about how to place adsorbates on it.
     """
 
-    # TODO (wardlt): Be able to support >1 surface for different catalysis
+    # TODO (wardlt): Be able to support >1 surfaces for different catalysis
     # TODO (wardlt): Consider how to prioritize the different required calculations across surfaces
+    # TODO (wardlt): Determine how to select molecule orientation
     def __init__(self, surface_name: str, config_name: str):
         super().__init__("adsorption_energy", f"{surface_name}-config_name")
         self.surface_name = surface_name