3:['Cu1_3','Cu2_3']} for i in range(num_surface_slabs): for j in range(n_substrate_layers): globals()['atm_gp_surface_{}_layer_{}'.format( map_layer_index[j + 1], i + 1)] = model.AtomGroup() for id in map_layer_atoms[j + 1]: globals()['atm_gp_surface_{}_layer_{}'.format( map_layer_index[j + 1], i + 1)].add_atom(globals()['surface_{}'.format(i + 1)], id) #/substrate/end# #/atmgroup/end# #/sorbatesym/begin# n_sym = 16 for i in range(num_sorbate_slabs): globals()['sorbate_syms_{}'.format(i+1)] = [model.SymTrans([[1,0],[0,1]]), model.SymTrans([[1,0],[0,1]],t=[0.5,0.5]),\ model.SymTrans([[0,1],[1,0]]), model.SymTrans([[0,1],[1,0]],t=[0.5,0.5]), \ model.SymTrans([[0,1],[-1,0]]), model.SymTrans([[0,1],[-1,0]],t=[0.5,0.5]),\ model.SymTrans([[-1,0],[0,1]]),model.SymTrans([[-1,0],[0,1]],t=[0.5,0.5]),\ model.SymTrans([[-1,0],[0,-1]]),model.SymTrans([[-1,0],[0,-1]],t=[0.5,0.5]),\ model.SymTrans([[0,-1],[-1,0]]),model.SymTrans([[0,-1],[-1,0]],t=[0.5,0.5]),\ model.SymTrans([[0,-1],[1,0]]),model.SymTrans([[0,-1],[1,0]],t=[0.5,0.5]),\ model.SymTrans([[1,0],[0,-1]]),model.SymTrans([[1,0],[0,-1]],t=[0.5,0.5])][0:n_sym] #/sorbatesym/end# #/sample/begin# surface_parms = {'delta1': 0., 'delta2': 0.} domains = {} for i in range(num_surface_slabs): domains['domain{}'.format(i + 1)] = {} domains['domain{}'.format(i +
for i in range(num_surface_slabs): for j in range(n_substrate_layers): globals()['atm_gp_surface_{}_layer_{}'.format( map_layer_index[j + 1], i + 1)] = model.AtomGroup() for id in map_layer_atoms[j + 1]: globals()['atm_gp_surface_{}_layer_{}'.format( map_layer_index[j + 1], i + 1)].add_atom(globals()['surface_{}'.format(i + 1)], id) #/substrate/end# #/atmgroup/end# #/sorbatesym/begin# n_sym = 1 for i in range(num_sorbate_slabs): globals()['sorbate_syms_{}'.format(i + 1)] = [ model.SymTrans([[1, 0], [0, 1]]), model.SymTrans([[0, 1], [-1, 0]]), model.SymTrans([[1, 0], [0, 1]]), model.SymTrans([[0, -1], [1, 0]]) ][0:n_sym] #/sorbatesym/end# #/sample/begin# domains = {} for i in range(num_surface_slabs): domains['domain{}'.format(i + 1)] = {} domains['domain{}'.format(i + 1)]['slab'] = globals()['surface_{}'.format(i + 1)] domains['domain{}'.format(i + 1)]['sorbate'] = globals()[ 'sorbate_{}'.format(i + 1)]