Box¶

class poresim.box.Box(name='box', label=None)¶

This class creates a hypothetical simulation box, to which molecules are added. Furthermore, all properties like temperature and specific job properties can be adjusted separate from the global simulation values.

Parameters:

namestring, optional: Simulation name
labelNone, string, optional: Job identification label

Methods

`add_box`(link)	Set simulation box structure link.
`add_charge_si`(charge)	Add silicon charge for grid-atoms
`add_mol`(short, link, inp[, num_atoms, ...])	Add a molecule to the simulation box.
`add_pore`(link)	Add pore object to structure folder.
`add_struct`(ident, link)	Add file link to the structure dictionary.
`add_topol`(link[, top_type])	Add simulation topology files to simulation dictionary.
`get_job`()	Return the dictionary containing all simulation information.
`get_label`()	Return the simulation label.
`get_mols`()	Return list of molecule numbers to be filled in the box.
`get_name`()	Return the simulation box name.
`get_param`()	Return the dictionary containing all systems parameters.
`get_sim_dict`()	Return the simulation dictionary.
`get_struct`()	Return list of structure files.
`get_topol`()	Return list of topology files.
`set_job`(job)	Set the dictionary containing all simulation information.
`set_label`(label)	Set the simulation box label, for job identification.
`set_name`(name)	Set the simulation box name.
`set_param`(param)	Set the dictionary containing all systems parameters.
`set_sim_dict`(sim_dict)	Set the simulation dictionary.