Révision 69d17e8b modules/calculation.py

b/modules/calculation.py
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logger = logging.getLogger('DockOnSurf')
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def check_bak(file_name):


  		





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    """Checks if a file already exists and backs it up if so.


  		





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    @param file_name: file to be checked if exists


  		





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    """


  		





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    new_name = file_name


  		





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    bak_num = 0


  		





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    while os.path.isdir(new_name) or os.path.isfile(new_name):


  		





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        bak_num += 1


  		





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        new_name = new_name.split(".bak")[0] + f".bak{bak_num}"


  		





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    if bak_num > 0:


  		





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        os.rename(file_name, new_name)


  		





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        logger.warning(f"'{file_name}' already present. Backed it up to "


  		





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                       f"{new_name}")


  		





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def prep_cp2k(inp_file, run_type, atms_list):  # TODO name to PROJECT_NAME


  		





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    """Prepares the directories to run isolated calculation with CP2K.


  		





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    from shutil import copy


  		





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    import ase.io


  		





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    from pycp2k import CP2K


  		





  
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    from utilities import check_bak


  		





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    cp2k = CP2K()


  		





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    cp2k.parse(inp_file)


  		





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    force_eval = cp2k.CP2K_INPUT.FORCE_EVAL_list[0]


  		





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    @param atms_list: List of ase.Atoms objects containing the sets of atoms


  		





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    aimed to run the calculations of.


  		





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    """


  		





  
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    from utilities import check_bak


  		





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    run_types = ['isolated', 'screening', 'refinement']


  		





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    run_type_err = f"'run_type' must be one of the following: {run_types}"


  		





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    if not isinstance(run_type, str) or run_type.lower() not in run_types:


  		












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