Python SymTrans Examples

Example #1

File: template_script_Cu.py Project: jackey-qiu/DaFy

                   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 +

Example #2

File: model_script_standard_Cu.py Project: jackey-qiu/DaFy

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)]