Sample¶

class poreana.sample.Sample(system, link_traj, mol, atoms=[], masses=[], entry=0.5)¶

This class samples a trajectory to determine different properties. Different properties can be initialized to be run at the same time during the sampling run. The output is stored in form of pickle files for later calculation using methods provided in the package.

It is advisable to run the sampling on a cluster due to a high time and resource consumption.

The system can either be a pore system - variable system is a file link to the pore_system object file - or a simple simulation box - variable system is a list containing the dimensions in nano meter.

Parameters:

systemstring, list: Link to poresystem object file or a list of dimensions for a simple box analysisd
link_trajstring: Link to trajectory file (trr or xtc)
molMolecule: Molecule to calculate the density for
atomslist, optional: List of atom names, leave empty for whole molecule
masseslist, optional: List of atom masses, leave empty to read molecule object masses
entryfloat, optional: Remove pore entrance from calculation

Methods

`_angle`(data, region, dist, com, pos, pore_id)	This function calculates the angle between a molecule vector defined between two atoms and the surface normal vector at the postition of the molecules center of mass.
`_angle_data`()	Create angle data structure.
`_bin_ex`(bin_num)	This function creates a simple bin structure for the exterior of the pore based on the reservoir length.
`_bin_in`(bin_num)	This function creates a simple bin structure for the interior of the pore based on the pore diameter.
`_bin_in_const_A`(bin_num)	This function creates a bin structure for the interior of the pore based on the pore diameter so that all bins have the same area.
`_bin_in_slit`(bin_num)	This function creates a simple bin structure for the interior of the pore based on the pore diameter.
`_bin_mc`(bin_num, direction)	This function creates a simple bin structure for the pore and resevoir.
`_bin_window`(bin_num, len_window)	This function creates window list for each bin for the interior of the pore based on the pore diameter.
`_density`(data, region, dist, com, pore_id)	This function samples the density inside and outside of the pore.
`_density_data`()	Create density data structure.
`_diffusion_bin`(data, region, pore_in, dist, ...)	This function samples the mean square displacement of a molecule group in a pore in both axial and radial direction separated in radial bins.
`_diffusion_bin_data`()	Create bin diffusion data structure.
`_diffusion_bin_step`(idx)	Helper function to define allowed bin step list.
`_diffusion_mc`(data, idx_list, com, res_id, ...)	This function sample the transition matrix for the diffusion calculation with the Monte Carlo diffusion methode for a cubic simulation box.
`_diffusion_mc_data`()	Create mc diffusion data structure.
`_gyration`(data, region, dist, com, pos, pore_id)	This function calculates the gyration radius of molecules inside the pore.
`_gyration_data`()	Create gyration data structure.
`_sample_helper`(frame_list, shift, is_pbc, ...)	Helper function for sampling run.
`init_angle`(link_out, vector_atoms[, ...])	Enable angle sampling routine.
`init_density`(link_out[, bin_num, ...])	Enable density sampling routine.
`init_diffusion_bin`(link_out[, bin_num, ...])	Enable diffusion sampling routine.
`init_diffusion_mc`(link_out, len_step[, ...])	Enable diffusion sampling routine with the MC Alogrithm.
`init_gyration`(link_out[, bin_num])	Enable gyration sampling routine.
`sample`([shift, np, is_pbc, is_broken, ...])	This function runs all enabled sampling routines.