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
Changed the number of conformers for which to warn the user to be greater than 1 and not 0
Added cp2k.inp and cp2k.sub
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.
Deleted test_confs_to_mol_list as now it is in test_formats.py.
Added tests for 'confs_to_mol_list' and 'rdkit_mol_to_ase_atoms' functions. Reformated the import of modules in the test.
Added tests for the reading of subm_script and project_name options. Changed tests/isolated.inp to tests/cp2k.inp as its content is irrelevant for testing. Reformated the import of modules in the test.
Added a warning when a mol object with more than one conformer is parsed to the rdkit_mol_to_ase_atoms function. Extended confs_to_mol_list documentation
Removed 'project_name' from the mandatory options
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.
Check if the input file of the code used for calculations is readable by the relevant library. Removed project_name from the mandatory options in Global.
Removed non used options from input and added new option on tests
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
Changed logging of formats.py from info to debug severity level.
Corrected argument of prep_iso and improved code documentation
Raise an error if clustering does not converge
Created calculation.py module and moved prep_run from isolated.py to it
Included printing the number of conformers generated and reformat documentation in isolated.py
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