root / ase / io / sdf.py
Historique | Voir | Annoter | Télécharger (591 octet)
| 1 | 1 | tkerber | from math import pi, cos, sin, sqrt, acos |
|---|---|---|---|
| 2 | 1 | tkerber | |
| 3 | 1 | tkerber | from ase.atoms import Atoms |
| 4 | 1 | tkerber | from ase.parallel import paropen |
| 5 | 1 | tkerber | |
| 6 | 1 | tkerber | def read_sdf(fileobj): |
| 7 | 1 | tkerber | if isinstance(fileobj, str): |
| 8 | 1 | tkerber | fileobj = open(fileobj)
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| 9 | 1 | tkerber | |
| 10 | 1 | tkerber | lines = fileobj.readlines() |
| 11 | 1 | tkerber | # first three lines header
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| 12 | 1 | tkerber | del lines[:3] |
| 13 | 1 | tkerber | |
| 14 | 1 | tkerber | #
|
| 15 | 1 | tkerber | L1 = lines.pop(0).split()
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| 16 | 1 | tkerber | natoms = int(L1[0]) |
| 17 | 1 | tkerber | positions = [] |
| 18 | 1 | tkerber | symbols = [] |
| 19 | 1 | tkerber | for line in lines[:natoms]: |
| 20 | 1 | tkerber | x, y, z, symbol = line.split()[:4]
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| 21 | 1 | tkerber | symbols.append(symbol) |
| 22 | 1 | tkerber | positions.append([float(x), float(y), float(z)]) |
| 23 | 1 | tkerber | return Atoms(symbols=symbols, positions=positions) |