def freeze_center(slab):
sf = AdsorbateSiteFinder(slab)
surf_sites = sf.find_surface_sites_by_height(slab, height=5, bottom=True)
sd_lst = []
for site in slab:
if site in surf_sites:
sd_lst.append([True, True, True])
else:
sd_lst.append([False, False, False])
slab.add_site_property('selective_dynamics', sd_lst)
return slab
def determine_coverage(slab, coverage, ref_species=None, height=2.1):
sf = AdsorbateSiteFinder(slab)
surf_sites = sf.find_surface_sites_by_height(slab, height=height)
if ref_species == None:
n_surf_atoms = len(surf_sites)
else:
n_surf_atoms = 0
for site in surf_sites:
if site.species_string == ref_species:
n_surf_atoms += 1
# print(n_surf_atoms)
n_sites_init = n_surf_atoms*coverage
n_sites = np.round(n_sites_init)
if n_sites != n_sites_init:
actual_coverage = n_sites/n_surf_atoms
print('Warning: the number of sites used does not exactly match the specified coverage, the actual coverage is %s' %actual_coverage)
else:
actual_coverage = coverage
n_sites = int(n_sites)
return n_sites, actual_coverage
