def build_instance(cls,xyzu_oc_m = [0.5, 0.5, 1.5, 0.1, 1, 1], els = ['O','C','C','O'], flat_down_index = [2],anchor_index_list = [1, None, 1, 2 ], lat_pars = [3.615, 3.615, 3.615, 90, 90, 90]):
domain = model_2.Slab(T_factor = 'u')
ids_all = deepcopy(els)
for each in set(els):
index_temp_all = list(np.where(np.array(els) == each)[0])
for index_temp in index_temp_all:
ids_all[index_temp] = "{}{}".format(ids_all[index_temp], index_temp_all.index(index_temp)+1)
for i in range(len(ids_all)):
domain.add_atom(ids_all[i],els[i],*xyzu_oc_m)
ids = deepcopy(ids_all)
del(ids[anchor_index_list.index(None)])
anchor_id = ids_all[anchor_index_list.index(None)]
flat_down_index_new = [[i,i-1][int(i>anchor_index_list.index(None))] for i in flat_down_index]
r_list_names = []
gamma_list_names = []
delta_list_names = []
for i in range(len(anchor_index_list)):
each = anchor_index_list[i]
if each != None:
#if i not in flat_down_index:
delta_list_names.append("delta_{}_{}".format(ids_all[i],ids_all[each]))
if each != None:
r_list_names.append("r_{}_{}".format(ids_all[i],ids_all[each]))
gamma_list_names.append("gamma_{}_{}".format(ids_all[i],ids_all[each]))
rgh = UserVars()
rgh.new_var('gamma',0)
rgh.new_var('rot_ang_x',0)
rgh.new_var('rot_ang_y',0)
for r in r_list_names:
rgh.new_var(r, 1.5)
for i in range(len(delta_list_names)):
delta = delta_list_names[i]
if i in flat_down_index_new:
rgh.new_var(delta, 0)
else:
rgh.new_var(delta, 20)
#for gamma in gamma_list_names:
# rgh.new_var(gamma, 10)
instance = cls(domain, ids, anchor_id, flat_down_index = flat_down_index_new, lat_pars = lat_pars)
instance.rgh = rgh
instance.r_list_names = r_list_names
instance.delta_list_names = delta_list_names
instance.gamma_list_names = gamma_list_names
instance.gamma_handedness = [1]*anchor_index_list.index(None)+[0]*(len(anchor_index_list)-anchor_index_list.index(None)-1)
instance.new_anchor_list = [ids_all[i] for i in anchor_index_list if i!=None]
instance.rot_ang_x_list = [0] * len(instance.ids)
instance.rot_ang_y_list = [0] * len(instance.ids)
return instance
Egam = 6.626 * (10**-34) * 3 * (
10**8) / wal * 10**10 / 1.602 * 10**19 #energy in ev
LAM = 1.5233e-22 * Egam**6 - 1.2061e-17 * Egam**5 + 2.5484e-13 * Egam**4 + 1.6593e-10 * Egam**3 + 1.9332e-06 * Egam**2 + 1.1043e-02 * Egam
exp_const = 4 * kvect / LAM
auc = unitcell.a * unitcell.b * np.sin(unitcell.gamma)
#/expconstant/end#
#globalsetting/end#
#--set instrument--#
#/instrument/begin#
inst = model.Instrument(wavel=wal, alpha=2.0)
#/instrument/end#
#--set bulk slab--#
#/bulk/begin#
bulk = model.Slab()
bulk_file = 'Cu100_bulk.str'
tool_box.add_atom_in_slab(bulk, os.path.join(batch_path_head, bulk_file))
#/bulk/end#
#--set surface slabs--#
#/surfaceslab/begin#
surface_slab_head = 'Cu100_surface_'
use_same_tag = 1
for i in range(num_surface_slabs):
globals()['surface_{}'.format(i + 1)] = model.Slab(c=1.0)
if use_same_tag == None:
tag = i + 1
else:
tag = use_same_tag
tool_box.add_atom_in_slab(