Added pbc's as a instance attribute of Pynta. Fixed few places in cod…

…e to make sure the pbc's match what the user sets as the input.

pynta/calculator.py

@@ -159,6 +159,8 @@ def run_harmonically_forced_xtb_no_pbc(atoms,atom_bond_potentials,site_bond_pote
 
     target = atoms.cell[0][:2] + atoms.cell[1][:2]
 
+    og_pbc = atoms.pbc # Need to apply original pbc's on atoms object (depends on QC software)
+
     site_poss = []
     site_inds = []
     site_mols = []
@@ -302,7 +304,7 @@ def run_harmonically_forced_xtb_no_pbc(atoms,atom_bond_potentials,site_bond_pote
 
     outadslab = slab + newad
 
-    outadslab.pbc = (True,True,False)
+    outadslab.pbc = og_pbc
 
     return outadslab,Eharm,Fharm
 

pynta/main.py

@@ -62,7 +62,7 @@ def __init__(self,path,rxns_file,surface_type,metal,label,launchpad_path=None,fw
 
         if software.lower() == 'vasp':
             self.pbc = (True,True,True)
-        
+
         if software_kwargs_gas:
             self.software_kwargs_gas = software_kwargs_gas
         else:
@@ -131,7 +131,7 @@ def generate_slab(self,skip_launch=False):
             a = self.a
         #construct slab with optimial lattice constant
         slab = slab_type(self.metal,self.repeats,a,self.vacuum)
-        slab.pbc = (True, True, False)
+        slab.pbc = self.pbc
         write(os.path.join(self.path,"slab_init.xyz"),slab)
         self.slab_path = os.path.join(self.path,"slab.xyz")
         if self.software != "XTB":
@@ -252,7 +252,7 @@ def generate_initial_adsorbate_guesses(self,skip_structs=False):
             ads,mol_to_atoms_map = get_adsorbate(mol)
             if len(surf_sites) == 0:
                 if not skip_structs:
-                    ads.pbc = (True,True,False)
+                    ads.pbc = self.pbc
                     ads.center(vacuum=10)
                     structures[sm] = [ads]
                 gratom_to_molecule_atom_maps[sm] = {val:key for key,val in mol_to_atoms_map.items()}