Merge pull request #34 from zadorlab/pbc_attribute

Pbc attribute
zadorlab · Mar 22, 2024 · 92e8fdd · 92e8fdd
2 parents 9d4d0b9 + ec91f83
commit 92e8fdd
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git 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
@@ -24,7 +24,7 @@
 
 class Pynta:
     def __init__(self,path,rxns_file,surface_type,metal,label,launchpad_path=None,fworker_path=None,
-        vacuum=8.0,repeats=(3,3,4),slab_path=None,software="Espresso",socket=False,queue=False,njobs_queue=0,a=None,
+        vacuum=8.0,repeats=(3,3,4),slab_path=None,software="Espresso", pbc=(True,True,False),socket=False,queue=False,njobs_queue=0,a=None,
         software_kwargs={'kpts': (3, 3, 1), 'tprnfor': True, 'occupations': 'smearing',
                             'smearing':  'marzari-vanderbilt',
                             'degauss': 0.01, 'ecutwfc': 40, 'nosym': True,
@@ -49,6 +49,7 @@ def __init__(self,path,rxns_file,surface_type,metal,label,launchpad_path=None,fw
         self.slab_path = slab_path
         self.vacuum = vacuum
         self.a = a
+        self.pbc = pbc
         self.software = software
         self.socket = socket
         self.repeats = repeats
@@ -59,6 +60,9 @@ def __init__(self,path,rxns_file,surface_type,metal,label,launchpad_path=None,fw
         self.adsorbate_fw_dict = dict()
         self.software_kwargs = software_kwargs
 
+        if software.lower() == 'vasp':
+            self.pbc = (True,True,True)
+
         if software_kwargs_gas:
             self.software_kwargs_gas = software_kwargs_gas
         else:
@@ -127,7 +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":
@@ -248,7 +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()}