Révision ffa1b366 modules/calculation.py
| b/modules/calculation.py | ||
|---|---|---|
| 15 | 15 |
""" |
| 16 | 16 |
from glob import glob |
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import ase.io |
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from pycp2k import CP2K |
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from modules.utilities import tail |
| 19 | 20 |
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finished_calcs = [] |
| 21 | 22 |
unfinished_calcs = [] |
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for conf in sorted(os.listdir(run_type), key=_human_key): |
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if not os.path.isdir(f'{run_type}/{conf}') or 'conf_' not in conf:
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conf_path = f'{run_type}/{conf}'
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if not os.path.isdir(conf_path) or 'conf_' not in conf: |
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| 24 | 26 |
continue |
| 25 | 27 |
if code == 'cp2k': |
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out_file_list = glob(f"{run_type}/{conf}/*.out")
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restart_file_list = glob(f"{run_type}/{conf}/*-1.restart")
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if len(out_file_list) == 0 or len(restart_file_list) == 0: |
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cp2k = CP2K() |
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restart_file_list = glob(f"{conf_path}/*-1.restart")
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if len(restart_file_list) == 0: |
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logger.warning(f"No *-1.restart file found on {conf_path}.")
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unfinished_calcs.append(conf) |
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elif len(out_file_list) > 1 or len(restart_file_list) > 1: |
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warn_msg = f'There is more than one file matching the {code} ' \
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f'pattern for finished calculation (*.out / ' \ |
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f'*-1.restart) in {run_type}/{conf}: ' \
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f'{out_file_list, restart_file_list}. ' \
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f'Skipping directory.' |
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continue |
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elif len(restart_file_list) > 1: |
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warn_msg = f'There is more than one CP2K restart file ' \ |
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f'(*-1.restart / in {conf_path}: ' \
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f'{restart_file_list}. Skipping directory.'
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unfinished_calcs.append(conf) |
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logger.warning(warn_msg) |
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continue |
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out_files = [] |
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for file in os.listdir(conf_path): |
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with open(conf_path+"/"+file, "rb") as out_fh: |
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tail_out_str = tail(out_fh) |
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if tail_out_str.count("PROGRAM STOPPED IN") == 1:
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out_files.append(file) |
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if len(out_files) > 1: |
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warn_msg = f'There is more than one CP2K output file in ' \ |
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f'{conf_path}: {out_files}. Skipping directory.'
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logger.warning(warn_msg) |
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unfinished_calcs.append(conf) |
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elif len(out_files) == 0: |
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warn_msg = f'There is no CP2K output file in {conf_path}. ' \
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'Skipping directory.' |
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| 36 | 55 |
logger.warning(warn_msg) |
| 37 | 56 |
unfinished_calcs.append(conf) |
| 38 | 57 |
else: |
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with open(out_file_list[0], 'rb') as out_fh: |
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if "PROGRAM STOPPED IN" not in tail(out_fh): |
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unfinished_calcs.append(conf) |
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else: |
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finished_calcs.append(conf) |
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finished_calcs.append(conf) |
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| 44 | 59 |
elif code == 'vasp': |
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out_file_list = glob(f"{run_type}/{conf}/OUTCAR")
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out_file_list = glob(f"{conf_path}/OUTCAR")
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| 46 | 61 |
if len(out_file_list) == 0: |
| 47 | 62 |
unfinished_calcs.append(conf) |
| 48 | 63 |
elif len(out_file_list) > 1: |
| 49 | 64 |
warn_msg = f'There is more than one file matching the {code} ' \
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| 50 | 65 |
f'pattern for finished calculation (*.out / ' \ |
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f'*-1.restart) in {run_type}/{conf}: ' \
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f'*-1.restart) in {conf_path}: ' \
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| 52 | 67 |
f'{out_file_list}. Skipping directory.'
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| 53 | 68 |
logger.warning(warn_msg) |
| 54 | 69 |
unfinished_calcs.append(conf) |
| 55 | 70 |
else: |
| 56 | 71 |
try: |
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ase.io.read(f"{run_type}/{conf}/OUTCAR")
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ase.io.read(f"{conf_path}/OUTCAR")
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| 58 | 73 |
except ValueError: |
| 59 | 74 |
unfinished_calcs.append(conf) |
| 60 | 75 |
continue |
| 61 | 76 |
except IndexError: |
| 62 | 77 |
unfinished_calcs.append(conf) |
| 63 | 78 |
continue |
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with open(f"{run_type}/{conf}/OUTCAR", 'rb') as out_fh:
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with open(f"{conf_path}/OUTCAR", 'rb') as out_fh:
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| 65 | 80 |
if "General timing and accounting" not in tail(out_fh): |
| 66 | 81 |
unfinished_calcs.append(conf) |
| 67 | 82 |
else: |
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