From 8495d128058f5760a85562b8e726f75224191b89 Mon Sep 17 00:00:00 2001 From: Georg Kastlunger Date: Tue, 14 May 2024 19:56:08 +0200 Subject: [PATCH] Not transferring inhomogeneous list into array as it fails --- catkit/gen/adsorption.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/catkit/gen/adsorption.py b/catkit/gen/adsorption.py index 3c24af16..b150132f 100644 --- a/catkit/gen/adsorption.py +++ b/catkit/gen/adsorption.py @@ -57,8 +57,6 @@ def __init__(self, slab, surface_atoms=None, tol=1e-5): self.coordinates = np.array(self.coordinates) self.connectivity = np.array(self.connectivity, dtype=int) - self.r1_topology = np.array(self.r1_topology) - self.r2_topology = np.array(self.r2_topology) self.frac_coords = np.dot(self.coordinates, np.linalg.pinv(slab.cell)) self.slab = slab @@ -307,8 +305,8 @@ def get_adsorption_vectors(self, unique=True, screen=True): else: sel = self.get_periodic_sites(screen=screen) coords = self.coordinates[sel] - r1top = self.r1_topology[sel] - r2top = self.r2_topology[sel] + r1top = [self.r1_topology[i] for i in sel] + r2top = [self.r2_topology[i] for i in sel] vectors = np.empty((coords.shape[0], 3)) for i, s in enumerate(coords):