pysimm.apps.zeopp

Module Contents

Functions

network(s, **kwargs)

pysimm.apps.zeopp.network

Attributes

ZEOpp_EXEC

pysimm.apps.zeopp.ZEOpp_EXEC[source]
pysimm.apps.zeopp.network(s, **kwargs)[source]

pysimm.apps.zeopp.network

Perform 1. Pore diameters; 2. Channel identification and dimensionality; 3. Surface area;

  1. Accessible volume; 5. Pore size distribution calculation using zeo++ v2.2

with options to do 6. Probe-occupiable volume; 7. Stochastic ray tracing; 8. Blocking spheres;

  1. Distance grids; 10. Structure analysis

Parameters

  • s – pysimm System object or filename of file in CSSR | CUC | V1 | CIF format

  • atype_name – True to use atom type as atom name (usually need radii and mass info), False to use atom element

  • radii – file name that contain atom radii data (rad.rad)

  • mass – file name that contain atom mass data (mass.mass)

  • probe_radius – radius of a probe used in sampling of surface (1.2 A)

  • chan_radius – radius of a probe used to determine accessibility of void space (1.2 A)

  • num_samples – number of Monte Carlo samples per unit cell (50000)

  • simulation (option to include in the) –

    set True to activate ha: default=True, for using high accuracy, res: default=True, for diameters of the largest included sphere, the largest free sphere and the largest included sphere along free sphere path chan: default=True, for channel systems characterized by dimensionality as well as Di, Df and Dif sa: default=True, for surface area accessible to a spherical probe, characterized by

    accessible surface area (ASA) and non-accessible surface area (NASA)

    vol: default=True, for accessible volume (AV) and non-accessible volume (NAV) volpo: default=False, for accessible proce-occupiable volume (POAV) and non-accessible probe-occupiable volume (PONAV) psd: default=True, for the “deriviative distribution” (change of AV w.r.t probe size) reported in the histogram file with 1000 bins of size of 0.1 Ang ray_atom: default=False block: default=False extra: user provided options, such as -gridG, -gridBOV, -strinfo, -oms, etc.

ZEOpp_EXEC: path to zeo++ executable (network)

Returns

None