Révision ae097639 modules/screening.py
| b/modules/screening.py | ||
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| 112 | 112 |
return np.array([np.average(array[:, i]) for i in range(num_vects)]) |
| 113 | 113 |
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| 114 | 114 |
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| 115 |
def get_atom_coords(atoms: ase.Atoms, ctrs_list=None):
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"""Gets the coordinates of the specified indices from a ase.Atoms object.
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def get_atom_coords(atoms: ase.Atoms, center=None):
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"""Gets the coordinates of the specified center for an ase.Atoms object.
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| 117 | 117 |
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| 118 |
Given an ase.Atoms object and a list of atom indices specified in ctrs_list |
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it gets the coordinates of the specified atoms. If the element in the |
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ctrs_list is not an index but yet a list of indices, it computes the |
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If center is not an index but a list of indices, it computes the |
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| 121 | 119 |
element-wise mean of the coordinates of the atoms specified in the inner |
| 122 | 120 |
list. |
| 123 | 121 |
@param atoms: ase.Atoms object for which to obtain the coordinates of. |
| 124 |
@param ctrs_list: list of (indices/list of indices) of the atoms for which
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| 125 |
the coordinates should be extracted.
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@param center: index/list of indices of the atoms for which the coordinates
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should be extracted. |
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| 126 | 124 |
@return: np.ndarray of atomic coordinates. |
| 127 | 125 |
""" |
| 128 |
coords = [] |
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err = "'ctrs_list' argument must be an integer, a list of integers or a " \ |
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"list of lists of integers. Every integer must be in the range " \ |
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"[0, num_atoms)" |
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if ctrs_list is None: |
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ctrs_list = range(len(atoms)) |
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elif isinstance(ctrs_list, int): |
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if ctrs_list not in range(len(atoms)): |
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logger.error(err) |
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raise ValueError(err) |
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return atoms[ctrs_list].position |
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for elem in ctrs_list: |
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if isinstance(elem, list): |
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coords.append(vect_avg([atoms[c].position for c in elem])) |
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elif isinstance(elem, int): |
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coords.append(atoms[elem].position) |
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else: |
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logger.error(err) |
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raise ValueError |
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return np.array(coords) |
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| 126 |
err_msg = "Argument 'ctr' must be an integer or a list of integers. "\ |
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"Every integer must be in the range [0, num_atoms)" |
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if center is None: |
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center = list(range(len(atoms))) |
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if isinstance(center, int): |
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if center not in list(range(len(atoms))): |
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logger.error(err_msg) |
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raise ValueError(err_msg) |
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return atoms[center].position |
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elif isinstance(center, list): |
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for elm in center: |
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if elm not in list(range(len(atoms))): |
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logger.error(err_msg) |
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raise ValueError(err_msg) |
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return vect_avg([atoms[idx].position for idx in center]) |
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else: |
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logger.error(err_msg) |
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raise ValueError(err_msg) |
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| 148 | 144 |
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| 149 | 145 |
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| 150 | 146 |
def compute_norm_vect(atoms, idxs, cell): |
| ... | ... | |
| 959 | 955 |
surf.set_cell(inp_vars['pbc_cell']) |
| 960 | 956 |
|
| 961 | 957 |
surf_ads_list = [] |
| 962 |
sites_coords = get_atom_coords(surf, sites)
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| 958 |
sites_coords = [get_atom_coords(surf, site) for site in sites]
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| 963 | 959 |
if coll_coeff is not False: |
| 964 | 960 |
surf_cutoffs = natural_cutoffs(surf, mult=coll_coeff) |
| 965 | 961 |
surf_nghbs = len(neighbor_list("i", surf, surf_cutoffs))
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| 966 | 962 |
else: |
| 967 | 963 |
surf_nghbs = 0 |
| 968 | 964 |
for i, conf in enumerate(conf_list): |
| 969 |
molec_ctr_coords = get_atom_coords(conf, molec_ctrs)
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molec_ctr_coords = [get_atom_coords(conf, ctr) for ctr in molec_ctrs]
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| 970 | 966 |
if inp_vars['pbc_cell'] is not False: |
| 971 | 967 |
conf.set_pbc(True) |
| 972 | 968 |
conf.set_cell(inp_vars['pbc_cell']) |
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