From ec91f833527336a0fec6df40c2ac1e3cecfb8ae1 Mon Sep 17 00:00:00 2001
From: tdprice-858 <>
Date: Wed, 30 Aug 2023 18:46:02 -0700
Subject: [PATCH] Added pbc's as a instance attribute of Pynta. Fixed few
 places in code to make sure the pbc's match what the user sets as the input.

---
 pynta/calculator.py | 4 +++-
 pynta/main.py       | 6 +++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/pynta/calculator.py b/pynta/calculator.py
index 81d4e351..5f446325 100644
--- a/pynta/calculator.py
+++ b/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
 
diff --git a/pynta/main.py b/pynta/main.py
index 6adbb266..861d6145 100644
--- a/pynta/main.py
+++ b/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()}