3.3. Directory Management

Warning

In case you are working with a cluster, be aware that the ‘~’ might not work threw job management. Prefere explicite location instead – /home/yourname instead of ~ !

GlobalParameter.general_path

Type [string]

The general path used to defined all the other path of the directory. By default, it will be set to the working directory. You may define the directory with or without the final ‘/’:

GP.general_path = '/home/user/MD/My_systeme/Frog_Analysis'
GP.general_path = '/home/user/MD/My_systeme/Frog_Analysis/'

If you want to not use this behaviour – for instance you want to define yourself every directory – you can set GP.general_path to ‘/’. You may also define the other directory attribute with a starting ‘//’. For instance, If you want to set the QM datas at: /scratch/myname/Datas/Frog/Water_QM

GP.general_path = '/home/user/MD/My_systeme/Whatever/'
GP.dir_torun_QM = '//scratch/myname/Datas/Frog/Water_QM'

Note

The general_path does not affect the location of the GP.MD_file_name_topology and GP.MD_file_name_traj.

GlobalParameter.dir_mol_times

Type [string]

The directory used to store the molecular properties for each time step. These data are not humain-readable intented. These datas can become heavy depending on the number of molecule, time step and the number of analysis required. The path is updated using the GP.general_path attribute. The default value is “Molecule_times”.

Example

If no GP.dir_mol_times is declared, the results are saved at GP.general_path/Molecule_times.

If GP.dir_mol_times = Datas/Molecule_in_time, the results are saved at : GP.general_path/Datas/Molecule_in_time

GlobalParameter.dir_torun_QM

Type [string]

The directory used to store the QM directories: the input script and the results. A large number of directory can be created if many QM simulations are required and thus occupied large amount of space eventhough each file (input file or the result) are small. These data are humain-readable and we strongly recommand to have a look from time to time. The path is updated using the GP.general_path attribute. The default value is “QM_Simulations”.

Example

If no GP.dir_torun_QM is declared, the results are saved at GP.general_path/QM_Simulations.

If you want to set the QM datas at: “/scratch/myname/Datas/Frog/Water_QM”, you have to set GP.dir_torun_QM = “/scratch/myname/Datas/Frog/Water_QM”.

Note

If possible, we recommand to set this directory to a place where the writting/openning of the files are easely efficient.

GlobalParameter.dir_submission_file

Type [string]

The directory used to store the script needed to launch the QM run on a cluster. A large number of file can be created if many QM simulations are required, but it should not occupy a large amount of space. These script are humain-readable. The path is updated using the GP.general_path attribute. The default value is “Submission_script”.

Example

If no GP.dir_submission_file is declared, the results are saved at GP.general_path/Submission_script.

If GP.dir_submission_file = Dir_sge/, the results are saved at : GP.general_path/Dir_sge