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Extended the documentation
Updated README.md and added TODO.
Corrected bug. prep_cp2k was taking the original input_file instead of the new one with the updated Project_name.
Added TODO
Simplified the reading of coordinates and energies and the selection of conformers.
Changed docstring and variable names in check_finished_calcs to improvea readability.
Implemented the automatic generation of POTCAR files.
Check for finished calculations is done without assuming output files are named *.out.
Submit jobs in human order.
Read directories in human order.
Centering molecule in the simulation cell to avoid problems at the screening stage.
Check that ase can read OUTCAR, else consider the calculation as unfinished.
Removed TODO.
Corrected error when creating creating files in configuration directories.
Corrected error when input file names contained the mandatory file name but it was not exactly the name (eg. 'INCAR-iso').
Implemented check on finished vasp calculation.
Added else clause for the scheduler/batch_quequing_system. Changed fallback values. Adjust docstrings, reformat code and other stylistic changes.
Implemented the possibility to run calculations with VASP.
Changed log message of Unrecognized job.
Unified the call of prep_cp2k for differ run_types
Change project_name value in cp2k input to be the project_name value in dockonsurf input plus the run_type.
Changed warning message
Implemented actual commands for LSF scheduler
Removed Capitalization on job name as it led to misunderstandings
Implemented new way to specify maximum jobs on running/pending status with only one keyword in the input. Reformat files.
Changed logger calls.
Changed order of the functions
Check restart file to be also present for the calculation to be finished.
Implemented check_finished_calcs which checks whether calculations are finished normally or not.
Implementes support for irene custom batch queuing system.
A maximum number of jobs can be set to, not only the pending ones, but now also the running ones.
Added variables for the chek of the job status in lsf. Added some comments and small code rearrangement.
Combined sub_sge and sub_lsf in a more generic function. Combined get_jobs_status_sge and get_jobs_status_lsf in a more generic function. Removed the dependency on gridtk.
Started implementing lsf jobs
Corrected log messages.
Reduced the molecule name length in the job_name.
Implemented refinement.py
Added punctuation marks at the end of every log messages.
Enabled the creation of calculation subdirectories and files when carrying out a dry run (batch_q_sys = None)
Check for options 'code', 'subm_script' is consistent with dry runs and running locally.
Correct indentation for all submitted jobs
Changed the import statement of internal libraries. Added logging to utilities.py
Moved check_bak from calculation.py to utilities.py and try_command from dos_input.py to utilities.py
Implemented function to read energies of a set of finished calculations. Implemented auxiliary function equivalent to bash tail. Reformat blank spaces and add TODO lines
Added 'local' and 'none' as possible batch queuing systems, to run calculations on the local computer and to not carry out the calculation at all (for debugging purposes).
Reorganized job submission, every batch_q_sys submitting function is directly called from run_calc. Updated requirements.txt
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