add better solvent placement logic

src/fairchem/data/oc/core/adsorbate_slab_config.py

@@ -489,20 +489,22 @@ def custom_tile_atoms(atoms: ase.Atoms):
     return new_atoms
 
 
-def get_interstitial_distances(adsorbate_slab_config: ase.Atoms):
+def get_interstitial_distances(adsorbate_slab_config: ase.Atoms, overlap_tag=2):
     """
-    Check to see if there is any atomic overlap between surface atoms
-    and adsorbate atoms.
+    Check to see if there is any atomic overlap between atoms with a particular
+    tag and all other atoms. Used to check overlap between adsorbate and
+    surface atoms.
 
     Args:
         adsorbate_slab_configuration (ase.Atoms): an slab atoms object with an
             adsorbate placed
+        overlap_tag (int): Tag to check overlap with
 
     Returns:
         (bool): True if there is atomic overlap, otherwise False
     """
     ads_slab_config = adsorbate_slab_config.copy()
-    mask = adsorbate_slab_config.get_tags() == 2
+    mask = adsorbate_slab_config.get_tags() == overlap_tag
     adsorbate_atoms = adsorbate_slab_config[mask]
     adsorbate_com = adsorbate_atoms.get_center_of_mass()
 
@@ -514,7 +516,7 @@ def get_interstitial_distances(adsorbate_slab_config: ase.Atoms):
     adsorbate_atoms = ads_slab_config[mask]
     adsorbate_elements = adsorbate_atoms.get_chemical_symbols()
 
-    mask = ads_slab_config.get_tags() == 1
+    mask = ads_slab_config.get_tags() != overlap_tag
     surface_atoms = ads_slab_config[mask]
     surface_elements = surface_atoms.get_chemical_symbols()
 
@@ -537,17 +539,20 @@ def get_interstitial_distances(adsorbate_slab_config: ase.Atoms):
     return post_radial_distances
 
 
-def there_is_overlap(adsorbate_slab_config: ase.Atoms):
+def there_is_overlap(adsorbate_slab_config: ase.Atoms, overlap_tag=2):
     """
     Check to see if there is any atomic overlap between surface atoms
     and adsorbate atoms.
 
     Args:
         adsorbate_slab_configuration (ase.Atoms): an slab atoms object with an
             adsorbate placed
+        overlap_tag (int): Tag to check overlap with
 
     Returns:
         (bool): True if there is atomic overlap, otherwise False
     """
-    post_radial_distances = get_interstitial_distances(adsorbate_slab_config)
+    post_radial_distances = get_interstitial_distances(
+        adsorbate_slab_config, overlap_tag
+    )
     return not all(np.array(post_radial_distances) >= 0)

src/fairchem/data/oc/core/interface_config.py

@@ -8,6 +8,7 @@
 
 import ase.io
 import numpy as np
+from fairchem.data.oc.core.adsorbate_slab_config import there_is_overlap
 from fairchem.data.oc.core.multi_adsorbate_slab_config import (
     MultipleAdsorbateSlabConfig,
 )
@@ -57,9 +58,6 @@ class InterfaceConfig(MultipleAdsorbateSlabConfig):
         well as the inter-adsorbate distance.
     vacuum_size: int
         Size of vacuum layer to add to both ends of the resulting atoms object.
-    solvent_interstitial_gap: float
-        Minimum distance, in Angstroms, between the solvent environment and the
-        adsorbate-slab environment.
     solvent_depth: float
         Volume depth to be used to pack solvents inside.
     pbc_shift: float
@@ -101,7 +99,6 @@ def __init__(
         num_configurations: int = 1,
         interstitial_gap: float = 0.1,
         vacuum_size: int = 15,
-        solvent_interstitial_gap: float = 2,
         solvent_depth: float = 8,
         pbc_shift: float = 0.0,
         packmol_tolerance: float = 2,
@@ -120,7 +117,6 @@ def __init__(
         self.ions = ions
         self.vacuum_size = vacuum_size
         self.solvent_depth = solvent_depth
-        self.solvent_interstitial_gap = solvent_interstitial_gap
         self.pbc_shift = pbc_shift
         self.packmol_tolerance = packmol_tolerance
 
@@ -159,12 +155,25 @@ def create_interface_on_sites(
             solvent_ions_atoms = self.create_packmol_atoms(geometry, n_solvent_mols)
             solvent_ions_atoms.set_cell(cell)
 
-            max_z = atoms.positions[:, 2].max() + self.solvent_interstitial_gap
-            translation_vec = cell[2]
-            translation_vec[2] = max_z
-            solvent_ions_atoms.translate(translation_vec)
+            # Place the solvent+ion environment at the interface with the
+            # adsorbate-slab envrionment. Iteratively tile the solvated atoms
+            # to ensure no atomic overlap with the adsorbate+slab.
+            # Take max slab height as starting point
+            max_slab_z = atoms[atoms.get_tags() == 1].positions[:, 2].max()
+            translation_vec = cell[2] / np.linalg.norm(cell[2])
+            overlap = True
+            while overlap:
+                _tv = translation_vec.copy()
+                _tv *= max_slab_z
+
+                _solvent_ions_atoms = solvent_ions_atoms.copy()
+                _solvent_ions_atoms.translate(_tv)
+
+                adslab = atoms.copy()
+                interface_atoms = adslab + _solvent_ions_atoms
+                overlap = there_is_overlap(interface_atoms, overlap_tag=3)
+                max_slab_z += 0.5  # iteratively tile cell
 
-            interface_atoms = atoms + solvent_ions_atoms
             interface_atoms.center(vacuum=self.vacuum_size, axis=2)
             interface_atoms.wrap()
 

tests/data/oc/tests/test_interface_config.py

@@ -22,7 +22,6 @@ def load_data(request):
     request.cls.ions = ions
     request.cls.vacuum = 15
     request.cls.solvent_depth = 10
-    request.cls.solvent_interstitial_gap = 2
 
 
 @pytest.mark.usefixtures("load_data")
@@ -38,7 +37,6 @@ def test_num_configurations(self):
             self.solvent,
             self.ions,
             vacuum_size=self.vacuum,
-            solvent_interstitial_gap=self.solvent_interstitial_gap,
             solvent_depth=self.solvent_depth,
             num_configurations=10,
         )
@@ -60,7 +58,6 @@ def test_solvent_density(self):
             self.solvent,
             self.ions,
             vacuum_size=self.vacuum,
-            solvent_interstitial_gap=self.solvent_interstitial_gap,
             solvent_depth=self.solvent_depth,
             num_configurations=10,
         )