Hi Hoffman,
as we all know, that Pt(111) has three adsorption site, on-top site, bridging site (between two atoms) and hollow sites (between three atoms).
However, in the kmos code package, the model of Pt(111) slabe just has two adsorption sites, hollow_1 and hollow_2. You give the example how to create Pt slab in kmos, the code shows below:
`#!/usr/bin/env python
"""Just a short incomplete demo for a non-orthogonal surface
Note how the process editor cannot correctly display non-orthogonal lattices. (as of v0.3)
"""
from kmos.types import
from kmos.io import
import numpy as np
pt = Project()
pt.set_meta(author='Max J. Hoffmann',
model_name='pt111',
email='mjhoffmann@gmail.com',
model_dimension=2,
debug=0)
Hi Hoffman, as we all know, that Pt(111) has three adsorption site, on-top site, bridging site (between two atoms) and hollow sites (between three atoms). However, in the kmos code package, the model of Pt(111) slabe just has two adsorption sites, hollow_1 and hollow_2. You give the example how to create Pt slab in kmos, the code shows below: `#!/usr/bin/env python """Just a short incomplete demo for a non-orthogonal surface
Note how the process editor cannot correctly display non-orthogonal lattices. (as of v0.3)
"""
from kmos.types import from kmos.io import import numpy as np
pt = Project() pt.set_meta(author='Max J. Hoffmann', model_name='pt111', email='mjhoffmann@gmail.com', model_dimension=2, debug=0)
pt.add_species(name='empty', color='#ffffff',) pt.add_species(name='H', representation="Atoms('H')", color='#ffff00')
layer = pt.add_layer(name='pt111',)
pt.lattice.representation = """[Atoms(symbols='Pt4', pbc=np.array([ True, True, False], dtype=bool), cell=np.array( [[ 2.77185858, 0. , 0. ], [ 1.38592929, 2.40049995, 0. ], [ 0. , 0. , 26.78963917]]), scaled_positions=np.array( [[0.0, 0.0, 0.37327863724326155], [0.33333333333333331, 0.33333333333333337, 0.45775954574775385], [0.66666666666666663, 0.66666666666666674, 0.54224045425224621], [0.0, 0.0, 0.62672136275673862]]), ),]"""
layer.sites.append(Site(name='hollow1', pos='0.333333333333 0.333333333333 0.672', default_species='default_species')) layer.sites.append(Site(name='hollow2', pos='0.666666666667 0.666666666667 0.672', default_species='default_species'))
pt.lattice.cell = np.array([[2.77185858, 0.0, 0.0], [1.38592929, 2.40049995, 0.0], [0.0, 0.0, 26.78963917]])
pt.add_parameter(name='T', adjustable=True, min=300, max=800, value=600)
pt.parse_and_add_process('H_adsorption_hollow1; empty@hollow1 -> H@hollow1; 100000') pt.parse_and_add_process('H_adsorption_hollow2; empty@hollow2 -> H@hollow2; 100000')
pt.parse_and_add_process('H_desorption_hollow1; H@hollow1 -> empty@hollow1; 100000') pt.parse_and_add_process('H_desorption_hollow2; H@hollow2 -> empty@hollow2; 100000')
pt.parse_and_add_process('H_diff_h1h2; H@hollow1 + empty@hollow2 -> empty@hollow1 + H@hollow2; 1000000000') pt.parse_and_add_process('H_diff_h2h1; H@hollow2 + empty@hollow1 -> empty@hollow2 + H@hollow1; 1000000000')
pt.filename = 'Pt_111.xml' pt.save() ` do I misunderstand?