allow acat surrogate_metal specification

zadorlab · Dec 20, 2023 · 160f9d2 · 160f9d2
1 parent 3076b4b
commit 160f9d2
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Showing 2 changed files with 11 additions and 5 deletions.
diff --git a/pynta/main.py b/pynta/main.py
@@ -35,7 +35,8 @@ def __init__(self,path,rxns_file,surface_type,metal,label,launchpad_path=None,fw
         TS_opt_software_kwargs=None,
         lattice_opt_software_kwargs={'kpts': (25,25,25), 'ecutwfc': 70, 'degauss':0.02, 'mixing_mode': 'plain'},
         reset_launchpad=False,queue_adapter_path=None,num_jobs=25,max_num_hfsp_opts=None,#max_num_hfsp_opts is mostly for fast testing
-        Eharmtol=3.0,Eharmfiltertol=30.0,Ntsmin=5,frozen_layers=2,fmaxopt=0.05,fmaxirc=0.1,fmaxopthard=0.05,c=None):
+        Eharmtol=3.0,Eharmfiltertol=30.0,Ntsmin=5,frozen_layers=2,fmaxopt=0.05,fmaxirc=0.1,fmaxopthard=0.05,c=None,
+        surrogate_metal=None):
 
         self.surface_type = surface_type
         if launchpad_path:
@@ -57,6 +58,10 @@ def __init__(self,path,rxns_file,surface_type,metal,label,launchpad_path=None,fw
         self.facet = metal + surface_type
         self.fws = []
         self.metal = metal
+        if surrogate_metal is None:
+            self.surrogate_metal = metal
+        else:
+            self.surrogate_metal = surrogate_metal
         self.adsorbate_fw_dict = dict()
         self.software_kwargs = software_kwargs
 
@@ -157,7 +162,7 @@ def analyze_slab(self):
         full_slab = self.slab
         cas = SlabAdsorptionSites(full_slab, self.surface_type,allow_6fold=False,composition_effect=False,
                         label_sites=True,
-                        surrogate_metal=self.metal)
+                        surrogate_metal=self.surrogate_metal)
 
         self.cas = cas
 
@@ -460,7 +465,7 @@ def setup_transition_states(self,adsorbates_finished=False):
                     "gratom_to_molecule_atom_maps":{sm: {str(k):v for k,v in d.items()} for sm,d in self.gratom_to_molecule_atom_maps.items()},
                     "gratom_to_molecule_surface_atom_maps":{sm: {str(k):v for k,v in d.items()} for sm,d in self.gratom_to_molecule_surface_atom_maps.items()},
                     "nslab":self.nslab,"Eharmtol":self.Eharmtol,"Eharmfiltertol":self.Eharmfiltertol,"Ntsmin":self.Ntsmin,
-                    "max_num_hfsp_opts":self.max_num_hfsp_opts})
+                    "max_num_hfsp_opts":self.max_num_hfsp_opts, "surrogate_metal":self.surrogate_metal})
             reactants = rxn["reactant_names"]
             products = rxn["product_names"]
             parents = []

diff --git a/pynta/tasks.py b/pynta/tasks.py
@@ -469,7 +469,7 @@ class MolecularTSEstimate(FiretaskBase):
     required_params = ["rxn","ts_path","slab_path","adsorbates_path","rxns_file","path","metal","facet",
                         "name_to_adjlist_dict", "gratom_to_molecule_atom_maps",
                         "gratom_to_molecule_surface_atom_maps","opt_obj_dict",
-                                "vib_obj_dict","IRC_obj_dict","nslab","Eharmtol","Eharmfiltertol","Ntsmin","max_num_hfsp_opts"]
+                                "vib_obj_dict","IRC_obj_dict","nslab","Eharmtol","Eharmfiltertol","Ntsmin","max_num_hfsp_opts","surrogate_metal"]
     optional_params = ["out_path","spawn_jobs","nprocs",]
     def run_task(self, fw_spec):
         gratom_to_molecule_atom_maps = {sm: {int(k):v for k,v in d.items()} for sm,d in self["gratom_to_molecule_atom_maps"].items()}
@@ -489,11 +489,12 @@ def run_task(self, fw_spec):
         Ntsmin = self["Ntsmin"]
         max_num_hfsp_opts = self["max_num_hfsp_opts"]
         slab_path = self["slab_path"]
+        surrogate_metal = self["surrogate_metal"]
         slab = read(slab_path)
 
         cas = SlabAdsorptionSites(slab,facet,allow_6fold=False,composition_effect=False,
                             label_sites=True,
-                            surrogate_metal=metal)
+                            surrogate_metal=surrogate_metal)
 
         adsorbates_path = self["adsorbates_path"]