Fix bug with listing of initial adsorption configs

LopezGroup-ICIQ · Sep 10, 2024 · 565881f · 565881f
1 parent a6c7a6a
commit 565881f
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Showing 2 changed files with 18 additions and 20 deletions.
diff --git a/src/care/evaluators/gamenet_uq/interface.py b/src/care/evaluators/gamenet_uq/interface.py
@@ -31,8 +31,8 @@
 
 class GameNetUQInter(IntermediateEnergyEstimator):
     def __init__(
-        self, 
-        surface: Surface, 
+        self,
+        surface: Surface,
         dft_db_path: Optional[str] = None,
         num_configs: int = 3,
         **kwargs
@@ -178,16 +178,14 @@ def eval(
             if self.db and self.retrieve_from_db(intermediate):
                 return
             else:
-                adsorptions = place_adsorbate(intermediate, self.surface)
+                adsorptions = place_adsorbate(intermediate, self.surface)[:self.num_configs]
                 ads_config_dict = {}
-                for i in range(len(adsorptions)):
-                    if i == self.num_configs:
-                        break
+                for i, adsorption in enumerate(adsorptions):
                     with no_grad():
                         ads_config_dict[f"{i}"] = {}
-                        ads_config_dict[f"{i}"]["ase"] = adsorptions[i]
+                        ads_config_dict[f"{i}"]["ase"] = adsorption
                         ads_config_dict[f"{i}"]["pyg"] = atoms_to_data(
-                            adsorptions[i], self.model.graph_params
+                            adsorption, self.model.graph_params
                         )
                         y = self.model(ads_config_dict[f"{i}"]["pyg"])
                         ads_config_dict[f"{i}"]["mu"] = (

diff --git a/src/care/evaluators/oc20models/interface.py b/src/care/evaluators/oc20models/interface.py
@@ -28,6 +28,10 @@ def __init__(
         cpu (bool): Whether to use the CPU for the calculation. Default is False.
         fmax (float): The maximum force allowed on the atoms. Default is 0.05 eV/Angstrom.
         max_steps (int): The maximum number of steps for the relaxation. Default is 100.
+
+        Note:
+
+        - The intermediate energy is stored as E_tot - E_slab in eV.
         """
 
         self.model_name = model_name
@@ -60,11 +64,7 @@ def eval(
         """
         gas_energy = intermediate['C']*self.eref['C'] + intermediate['H']*self.eref['H'] + intermediate['O']*self.eref['O']
 
-        if intermediate.phase == "surf":  # active site
-            intermediate.ads_configs = {
-                "surf": {"ase": intermediate.molecule, "mu": 0.0, "s": 0.0}
-            }
-        elif intermediate.phase == "gas":  # gas phase
+        if intermediate.phase == "gas":  # gas phase
             intermediate.ads_configs = {
                 "gas": {
                     "ase": intermediate.molecule,
@@ -74,14 +74,14 @@ def eval(
             }
         elif intermediate.phase == "ads":  # adsorbed
             ads_config_dict = {}
-            adsorptions = place_adsorbate(intermediate, self.surface)
-            for i in range(self.num_configs):
-                ads_config_dict[str(i)] = {}
-                adsorptions[i].set_calculator(self.calc)
-                opt = BFGS(adsorptions[i])
+            adsorptions = place_adsorbate(intermediate, self.surface)[:self.num_configs]
+            for i, adsorption in enumerate(adsorptions):
+                adsorption.set_calculator(self.calc)
+                opt = BFGS(adsorption)
                 opt.run(fmax=self.fmax, steps=self.max_steps)
-                ads_config_dict[str(i)]['ase'] = adsorptions[i]
-                ads_config_dict[str(i)]['mu'] = adsorptions[i].get_potential_energy() + gas_energy
+                ads_config_dict[str(i)] = {}
+                ads_config_dict[str(i)]['ase'] = adsorption
+                ads_config_dict[str(i)]['mu'] = adsorption.get_potential_energy() + gas_energy
                 ads_config_dict[str(i)]['s'] = 0.0
             intermediate.ads_configs = ads_config_dict
             print(intermediate.ads_configs)