def modify_geometry(g):
"""Modify the geometry according to the interface"""
if qtwrap.is_checked("remove_selected"): # remove some atoms
try:
inds = np.array(np.genfromtxt("REMOVE_ATOMS.INFO", dtype=np.int))
if inds.shape == (): inds = [inds]
except:
inds = [] # Nothing
print(inds)
g = sculpt.remove(g, inds) # remove those atoms
if qtwrap.is_checked("remove_single_bonded"): # remove single bonds
g = sculpt.remove_unibonded(g, iterative=True)
return g # return geometry
def pickup_hamiltonian():
if qtwrap.is_checked("do_scf"):
return hamiltonians.load() # load the Hamiltonian
else: # generate from scratch
return initialize()