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fragments.json
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{
"fragments" :
{
"OH" :
{
"mol_subset_atoms" : [0,1],
"selected_atom_index" : 0,
"molecule_axis" : "atoms 0 1",
"x_rot_angles" : [0],
"y_rot_angles" : [0, 90, -90],
"z_rot_angles" : [0, 90],
"vertical_angles" : "none",
"screening_atom_distance" : 1.5,
"screening_min_distance" : 1.0,
"fixed_indices_mol" : [0],
"fix_mol_xyz" : [0,0,1],
"dft_settings_override" : {
"vacuum" : {
"MAGMOM" : "2*0.6"
},
"adsorption" : {
}
}
},
"H" :
{
"mol_subset_atoms" : [2],
"selected_atom_index" : 2,
"molecule_axis" : "vector 1 0 0",
"x_rot_angles" : [0],
"y_rot_angles" : [0],
"z_rot_angles" : [0],
"vertical_angles" : "none",
"screening_atom_distance" : 1.5,
"screening_min_distance" : 1.0,
"fixed_indices_mol" : [0],
"fix_mol_xyz" : [0,0,1]
},
"O" :
{
"mol_subset_atoms" : [0],
"selected_atom_index" : 0,
"molecule_axis" : "vector 1 0 0",
"x_rot_angles" : [0],
"y_rot_angles" : [0],
"z_rot_angles" : [0],
"vertical_angles" : "none",
"screening_atom_distance" : 1.5,
"screening_min_distance" : 1.0,
"fixed_indices_mol" : [0],
"fix_mol_xyz" : [0,0,1]
}
},
"combinations": [
["mol", ["OH", "H"]],
["mol", ["O", "H", "H"]],
["OH", ["O", "H"]]
]
}