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check_bak function checks if the target file_name is a directory or a file instead of checking if the name is present on the cwd. prep_cp2k works with the filename instead of the whole absolute filepath. Changed the warning message accordingly
Unified all run_types inside the same function
Added fallback value for project_name in dos_input.py. Included log messages for submitted jobs on calculation.py, added TODO tasks and changed documentation on all three files.
Fix: the number of the submitted jobs now matches the number of conforemer id.
Wait for all jobs to finish.
Changed get_queued_jobs_sge to get_jobs_status_sge which now returns a list of job status instead of a list that were in qw status.
Added init_dir variable
Check if 'COORD_FILE_NAME' is defined in CP2K input file, and if not set to a default value. Fixed forgotten change of directory back to the initial directory.
The former create_bak_calc_dir function, now called check_bak, has generalized its behavior by checking if a file or directory exists and if so backs it up to a .bakX where X is a number such that bakX does not already exist.
Included 'project_name' on global mandatory options, corrected missing parentheses on str.capitalize method.
Added the submission of jobs to the SGE batch queuing system
Moved confs_to_mol_list function from isolated.py to formats.py module and generalised the calculations functions to be able to work with no matter which kind of calculation
Corrected argument of prep_iso and improved code documentation
Created calculation.py module and moved prep_run from isolated.py to it