Fix neighbour calc #207
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Fix neighbour calc #207
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apax/data/preprocessing.py
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| cell.flat[:: cell.shape[1] + 1] += 1 | ||
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what does this line do?
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same as cell[np.diag_indices_from(cell)] += 1 idk why I used that.
M-R-Schaefer
requested changes
Nov 14, 2023
apax/data/preprocessing.py
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| cell[idx, idx] = 1.0 | ||
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| cell.flat[:: cell.shape[1] + 1] += 1 |
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this could be replaced by something clearer
extend diagonal elements of cell
| @@ -119,7 +119,7 @@ def get_shrink_wrapped_cell(positions): | |||
| if cell[idx, idx] < 10e-1: | |||
| cell[idx, idx] = 1.0 | |||
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| cell.flat[:: cell.shape[1] + 1] += 1 | |||
| cell[np.diag_indices_from(cell)] += 1 | |||
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so the purpose of this line is to increase the cell by 1 Angstrom in all directions.
is this necessary?
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Yes. If the cell is too tight some atoms will be counted as being in a adjacent cell and the neighbour list will be wrong.
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I think 0.1 A would also be sufficient but I did not tested it.
M-R-Schaefer
approved these changes
Nov 14, 2023
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Addresses the problem that the shrink wrapped cell was too tight. Fix by adding a little layer if the shrink wrapped cell is created.