Basic Use

Importing pySoftWhere

import MDAnalysis as mda
import matplotlib.pyplot as plt
import numpy as np
import sys

Set the directory where pySoftWhere is located (if a full install has not been completed)

sys.path.append('<path to>/pysoftwhere')

Import the pySoftWhere functions

import pysoftwhere.clustering.cluster
import pysoftwhere.ICSI.icsi
import pysoftwhere.IPI.ipi

Intrinsic Planar Interface (IPI)

Firstly, define an MDAnalysis Universe

u = mda.Universe('system.tpr','system.xtc')

Now call pysoftwhere.IPI.ipi() to calculate the intrinsic density for a single frame

'''
u:           an MDAnalysis Universe that contains bond information
core_sel:    an MDAnalysis atom selection of the atoms used to construct the intrinsic interface
density_sel: an MDAnalysis atom selection of the atoms whose intrinsic positions will be calculated
interface:   'Lower' or 'Upper' - which interface of the core_sel to calculate with respect to
no_bins:     number of grid edges to use in each lateral dimension
recombine:   'True' or 'False' - set 'True' to recombine core_sel over the PBC in the vertical direction
cluster:     'True' or 'False' - set 'True' to check if any core_sel molecules have diffused away from the main selection and remove them from the analysis
interpolate_interface: 'True' or 'False' - set "True' to linearly interpolate the interface if it is patchy
'''

 intrinsic_z,interface_vals  =  pysoftwhere.IPI.ipi(u,
                                                    frame=-1,
                                                    core_sel='resname UNK and prop mass >2',
                                                    density_sel='name OW',
                                                    interface='Lower',
                                                    no_bins=51,
                                                    recombine=True,
                                                    cluster=True,
                                                    interpolate_interface=False)()

The pysoftwhere.IPI.ipi() function returns two results when called. These are intrinsic_z, a list of the intrinsic positions of atoms selected in density_sel, and interface_vals, an array containing the z-positions of the intrinsic interface.

Intrinsic Core-Shell Interface (ICSI)

Firstly, define an MDAnalysis Universe

u = mda.Universe('system.tpr','system.xtc')

Now call pysoftwhere.ICSI.icsi() to calculate the intrinsic density for a single frame. Note that pysoftwhere.ICSI.icsi() uses atomic positions, rather than an atom selection as used for IPI. This difference is made to allow flexibility that becomes useful in more complex use cases.

'''
u:           an MDAnalysis Universe that contains bond information
core_sel:    an MDAnalysis atom selection of the atoms used to construct the intrinsic interface
density_sel: an MDAnalysis atom selection of the atoms whose intrinsic positions will be calculated
interface:   'Lower' or 'Upper' - which interface of the core_sel to calculate with respect to
no_bins:     number of grid edges to use in each lateral dimension
recombine:   'True' or 'False' - set 'True' to recombine core_sel over the PBC in the vertical direction
cluster:     'True' or 'False' - set 'True' to check if any core_sel molecules have diffused away from the main selection and remove them from the analysis
interpolate_interface: 'True' or 'False' - set "True' to linearly interpolate the interface if it is patchy
'''


 intrinsic_r, spherical_r, icsi_vals = pysoftwhere.ICSI.icsi(u,

                                 cluster_resids=largest_cluster_resids,
                                 cluster_atoms_positions=cluster_atoms_positions,
                                 core_sel_atoms_positions=core_sel_atoms_positions,
                                 shell_sel_atoms_positions=shell_sel_atoms_positions,
                                 frame=ts.frame,
                                 no_bins=31,
                                 no_random_points=n_rand_points,
                                 normalisation_run=False)()

The pysoftwhere.IPI.ipi() function returns three results when called. These are intrinsic_r, a list of the intrinsic positions of atoms selected in density_sel, spherical_r, the radial distance of each density_sel atom to the nanoparticle center of mass, and icsi_vals, an array containing the r-positions of the intrinsic core-shell interface.