Révision cdc1edbe modules/formats.py
| b/modules/formats.py | ||
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| 172 | 172 |
return Atoms(symbols=symbols, positions=positions) |
| 173 | 173 |
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| 174 | 174 |
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def read_coords_vasp(file, spec_atoms=tuple()): |
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"""Reads the coordinates from VASP OUTCAR and returns an ase.Atoms object. |
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@param file: The file to read containing the coordinates. |
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@param spec_atoms: List of tuples containing the pairs of chemical symbols. |
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@return: ase.Atoms object of the coordinates in the file. |
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""" |
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import os |
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import ase.io |
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if not os.path.isfile(file): |
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err_msg = f"File {file} not found."
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logger.error(err_msg) |
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raise FileNotFoundError(err_msg) |
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if len(spec_atoms) > 0: |
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add_special_atoms(spec_atoms) |
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return ase.io.read(file) |
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| 175 | 193 |
def collect_coords(conf_list, code, run_type, spec_atms=tuple()): |
| 176 | 194 |
"""Directs the reading of coordinates on a set of subdirectories. |
| 177 | 195 |
|
| ... | ... | |
| 196 | 214 |
if code == 'cp2k': |
| 197 | 215 |
atoms_list.append(read_coords_cp2k(glob(f"{run_type}/{conf}/*-1"
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| 198 | 216 |
f".restart")[0], spec_atms)) |
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# elif code == 'vasp' |
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elif code == 'vasp': |
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atoms_list.append(read_coords_vasp(f"{run_type}/{conf}/OUTCAR",
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spec_atms)) |
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else: |
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err_msg = f"Collect coordinates not implemented for '{code}'."
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logger.error(err_msg) |
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raise NotImplementedError(err_msg) |
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| 200 | 224 |
return atoms_list |
| 201 | 225 |
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| 202 | 226 |
|
| ... | ... | |
| 239 | 263 |
if code == 'cp2k': |
| 240 | 264 |
energies.append(read_energy_cp2k( |
| 241 | 265 |
glob(f"{run_type}/{conf}/*.out")[0]))
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else: |
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err_msg = f"Collect energies not implemented for '{code}'."
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logger.error(err_msg) |
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raise NotImplementedError(err_msg) |
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| 242 | 270 |
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| 243 | 271 |
if len(energies) == 0: |
| 244 | 272 |
err = f"No results found on {run_type}"
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