Révision cdc1edbe
| b/modules/formats.py | ||
|---|---|---|
| 172 | 172 |
return Atoms(symbols=symbols, positions=positions) |
| 173 | 173 |
|
| 174 | 174 |
|
| 175 |
def read_coords_vasp(file, spec_atoms=tuple()): |
|
| 176 |
"""Reads the coordinates from VASP OUTCAR and returns an ase.Atoms object. |
|
| 177 |
|
|
| 178 |
@param file: The file to read containing the coordinates. |
|
| 179 |
@param spec_atoms: List of tuples containing the pairs of chemical symbols. |
|
| 180 |
@return: ase.Atoms object of the coordinates in the file. |
|
| 181 |
""" |
|
| 182 |
import os |
|
| 183 |
import ase.io |
|
| 184 |
if not os.path.isfile(file): |
|
| 185 |
err_msg = f"File {file} not found."
|
|
| 186 |
logger.error(err_msg) |
|
| 187 |
raise FileNotFoundError(err_msg) |
|
| 188 |
if len(spec_atoms) > 0: |
|
| 189 |
add_special_atoms(spec_atoms) |
|
| 190 |
return ase.io.read(file) |
|
| 191 |
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| 192 |
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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"
|
| 198 | 216 |
f".restart")[0], spec_atms)) |
| 199 |
# elif code == 'vasp' |
|
| 217 |
elif code == 'vasp': |
|
| 218 |
atoms_list.append(read_coords_vasp(f"{run_type}/{conf}/OUTCAR",
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|
| 219 |
spec_atms)) |
|
| 220 |
else: |
|
| 221 |
err_msg = f"Collect coordinates not implemented for '{code}'."
|
|
| 222 |
logger.error(err_msg) |
|
| 223 |
raise NotImplementedError(err_msg) |
|
| 200 | 224 |
return atoms_list |
| 201 | 225 |
|
| 202 | 226 |
|
| ... | ... | |
| 239 | 263 |
if code == 'cp2k': |
| 240 | 264 |
energies.append(read_energy_cp2k( |
| 241 | 265 |
glob(f"{run_type}/{conf}/*.out")[0]))
|
| 266 |
else: |
|
| 267 |
err_msg = f"Collect energies not implemented for '{code}'."
|
|
| 268 |
logger.error(err_msg) |
|
| 269 |
raise NotImplementedError(err_msg) |
|
| 242 | 270 |
|
| 243 | 271 |
if len(energies) == 0: |
| 244 | 272 |
err = f"No results found on {run_type}"
|
| b/modules/screening.py | ||
|---|---|---|
| 39 | 39 |
|
| 40 | 40 |
# Read properties |
| 41 | 41 |
if 'energy' in magns: |
| 42 |
conf_enrgs = collect_energies(calc_dirs, code, 'isolated') |
|
| 42 |
if code == 'cp2k': |
|
| 43 |
conf_enrgs = collect_energies(calc_dirs, code, 'isolated') |
|
| 44 |
elif code == 'vasp': |
|
| 45 |
conf_enrgs = np.array([conf.get_total_energy() |
|
| 46 |
for conf in orig_conf_list]) |
|
| 43 | 47 |
if 'moi' in magns: |
| 44 | 48 |
mois = np.array([conf.get_moments_of_inertia() for conf in conf_list]) |
| 45 | 49 |
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Formats disponibles : Unified diff