Révision 1e36f905 modules/calculation.py

b/modules/calculation.py
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    """
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    from modules.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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        run_type_err = f"'run_type' must be one of the following: {run_types}"
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        logger.error(run_type_err)
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        raise ValueError(run_type_err)
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  ......




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        logger.info(f"Doing a dry run of {run_type}.")


  		





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    check_bak(run_type)


  		





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    os.mkdir(run_type)


  		





  
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    # Prepare directories and files for relevant code.


  		





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    if inp_vars['code'] == 'cp2k':


  		





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        if run_type == 'isolated':


  		





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            prep_cp2k(inp_vars['isol_inp_file'], run_type, atms_list)


  		





  ......




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            prep_cp2k(inp_vars['refine_inp_file'], run_type, atms_list)


  		





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    # elif: inp_vars['code'] == 'Other codes here'


  		





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    # Submit/run Jobs


  		





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    if inp_vars['batch_q_sys'] == 'sge':


  		





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        stat_cmd = "qstat | grep %s | awk '{print $5}'"


  		





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        stat_dict = {'r': 'r', 'p': 'qw', 'f': ''}


  		





  ......




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                    stat_cmd, stat_dict, inp_vars['max_qw'],


  		





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                    inp_vars['project_name'])


  		





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    elif inp_vars['batch_q_sys'] == 'lsf':


  		





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        stat_cmd = "bjobs -w | grep %s | awk ''"


  		





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        submit_jobs(run_type, 'bsub', inp_vars['subm_script'],


  		





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                    inp_vars['max_qw'], inp_vars['project_name'])


  		





  
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        stat_cmd = "bjobs -w | grep %s | awk '{print $5}'"  # TODO Adapt to


  		





  
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        stat_dict = {'r': 'r', 'p': 'qw', 'f': ''} # TODO actual command


  		





  
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        submit_jobs(run_type, 'bsub -J %s %s', inp_vars['subm_script'],


  		





  
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                    stat_cmd, stat_dict, inp_vars['max_qw'],


  		





  
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                    inp_vars['project_name'])


  		





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    elif inp_vars['batch_q_sys'] == 'local':  # TODO implement local


  		





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        pass  # run_local


  		





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    elif inp_vars['batch_q_sys'] == 'none':


  		












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