Révision 0d7be691
| b/modules/add_adsorbate_euler+dissociation.py | ||
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| 9 | 9 |
from ase.io import read |
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from ase.io import write |
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from ase import Atom |
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from ase import Atoms |
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from ase import build |
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from ase.build import add_adsorbate |
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from ase import constraints |
| ... | ... | |
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angle = np.arccos(np.sign(norm_dot) if np.abs(norm_dot) >= 1 else norm_dot) |
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return(angle*180/np.pi if degrees else angle) |
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#################################################### |
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# Re-definition of the add-adsorbate function of ase |
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#################################################### |
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def new_add_adsorbate(slab, adsorbate, height, position=(0, 0, 0), offset=None, mol_index=0): |
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# works as the add_adsorbate fonction of ase but takes into account not only |
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# the x and y coordinates of the adsorption site but also the z in order to |
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# put the adsorbate at a given distance above the adsorption site (and not at |
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# a given height above the highest point of the surface) |
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# |
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# Sarah Blanck 22/01/2020 |
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info = slab.info.get('adsorbate_info', {})
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pos = np.array([0.0, 0.0]) # (x, y) part |
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pos2 = np.array([0.0, 0.0, 0.0]) # (x, y, z) part |
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spos = np.array([0.0, 0.0]) # part relative to unit cell |
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if offset is not None: |
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spos += np.asarray(offset, float) |
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if isinstance(position, basestring): |
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# A site-name: |
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if 'sites' not in info: |
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raise TypeError('If the atoms are not made by an ' + 'ase.build function, ' + 'position cannot be a name.')
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if position not in info['sites']: |
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raise TypeError('Adsorption site %s not supported.' % position)
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spos += info['sites'][position] |
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else: |
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pos2 += position |
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pos += [pos2[0], pos2[1]] |
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if 'cell' in info: |
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cell = info['cell'] |
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else: |
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cell = slab.get_cell()[:2, :2] |
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pos += np.dot(spos, cell) |
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# Convert the adsorbate to an Atoms object |
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if isinstance(adsorbate, Atoms): |
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ads = adsorbate |
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elif isinstance(adsorbate, Atom): |
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ads = Atoms([adsorbate]) |
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else: |
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# Assume it is a string representing a single Atom |
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ads = Atoms([Atom(adsorbate)]) |
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# Get the z-coordinate: |
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z = pos2[2] + height |
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# Move adsorbate into position |
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ads.translate([pos[0], pos[1], z] - ads.positions[mol_index]) |
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# Attach the adsorbate |
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slab.extend(ads) |
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########################################################### |
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# Definition of PBC conditions for molecules on the surface |
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########################################################### |
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def point_in_cell(p,h_matrix): |
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# This function checks wether a given point defined by [x,y,z] is inside a |
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# given cell defined by h_matrix=[a,b,c] where a=[xa,ya,za], b=[xb,yb,zb], |
| ... | ... | |
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return collision |
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########################################## |
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# Lecture des différents arguments de base |
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########################################## |
| ... | ... | |
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distance = distance - z_max_ads_1 + surf_atom_z |
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add_adsorbate(surface, molecule, distance, (x_atom_surf_1,y_atom_surf_1), mol_index=atom_molecule)
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new_add_adsorbate(surface, molecule, distance, (x_atom_surf_1,y_atom_surf_1,z_atom_surf_1), mol_index=atom_molecule)
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out=output+".xyz" |
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write(out, surface) |
| ... | ... | |
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else: |
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translation_matrix_dissociation.append(vector_H_diss) |
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molecule.translate(translation_matrix_dissociation) |
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add_adsorbate(surface, molecule, distance, (x_atom_surf_1,y_atom_surf_1), mol_index=atom_molecule)
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new_add_adsorbate(surface, molecule, distance, (x_atom_surf_1,y_atom_surf_1,z_atom_surf_1), mol_index=atom_molecule)
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output_diss = output + "_diss_" + str(i) + ".xyz" |
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write(output_diss, surface) |
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Formats disponibles : Unified diff