from ase.build import fcc111, add_adsorbate
from ase.atoms import Atoms
from ase.build import bulk
from ase.visualize import view
from blase.tools import get_bondpairs, write_blender
bulk = bulk('Pt')
bulk.write('pt.in')
adsorbate = Atoms('CO')
adsorbate[1].z = 1.1
atoms = fcc111('Pt', (2, 2, 3), a=3.96, vacuum=7.0)
add_adsorbate(atoms, adsorbate, 1.8, 'ontop')
# atoms = atoms*[5, 5, 1]
# view(atoms)
kwargs = {'show_unit_cell': 0,
'radii': 0.6,
'bond_cutoff': 1.0,
'display': True,
'make_real': True,
'outfile': 'figs/pt-111-co',
}
write_blender(atoms, **kwargs)
def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('inputfile',
type=str,
help="the input json file, includes coordinates of a \
set of points, threshold and a list of pairs of points "
)
parser.add_argument('--display',
action='store_true',
default=True,
help="render")
parser.add_argument('--run_render',
action='store_false',
default=False,
help="render")
parser.add_argument('--model',
'-m',
type=int,
default=0,
help="structure model")
parser.add_argument('--outfile',
'-o',
type=str,
default='output',
help="write output to specified file ")
parser.add_argument('--camera',
action='store_false',
default=False,
help="camera")
parser.add_argument('--light',
action='store_false',
default=False,
help="light")
parser.add_argument('--search_pbc_atoms',
action='store_false',
default=False,
help="search_pbc_atoms")
parser.add_argument('--search_molecule',
action='store_false',
default=False,
help="search_molecule")
args = parser.parse_args()
#
if args.inputfile.split('.')[-1] == 'cube':
atoms, data = read_cube_data(inputfile)
else:
atoms = read(args.inputfile)
if atoms.pbc.any():
kwargs['show_unit_cell'] = True
kwargs['display'] = args.display
kwargs['camera'] = args.camera
kwargs['light'] = args.light
kwargs['outfile'] = args.outfile + '.png'
kwargs['run_render'] = args.run_render
kwargs['search_pbc_atoms'] = args.search_pbc_atoms
kwargs['search_molecule'] = args.search_molecule
if args.model == 0:
kwargs['radii'] = 0.6
kwargs['bond_cutoff'] = 1.0
elif args.model == 1:
kwargs['bond_cutoff'] = None
elif args.model == 2:
kwargs['radii'] = 0.6
kwargs['bond_cutoff'] = 1.0
kwargs['polyhedral'] = {}
print('=' * 30)
print('Import structure')
print('=' * 30)
write_blender(atoms, **kwargs)
print('\n Finished!')
