pysimm.apps.zeopp module

pysimm.apps.zeopp.network(s, **kwargs)[source]
Perform:
  1. Pore diameters;
  2. Channel identification and dimensionality;
  3. Surface area;
  4. 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;
  9. Distance grids;
  10. Structure analysis
Parameters:

s (System) – pysimm System object or filename of file in CSSR | CUC | V1 | CIF format
Keyword Arguments:
 
  • atype_name (bool) – True to use atom type as atom name (usually need radii and mass info), False to use atom element (default: False)
  • radii (str) – file name that contain atom radii data (default: rad.rad)
  • mass (str) – file name that contain atom mass data (default: mass.mass)
  • probe_radius – radius of a probe used in sampling of surface (default: 1.2 A)
  • chan_radius – radius of a probe used to determine accessibility of void space (default: 1.2 A)
  • num_samples – number of Monte Carlo samples per unit cell (default: 50000) Other boolean options to include in the simulation (set True to activate)
  • ha – (default: True) switches on higher accuracy
  • res – (default: True) calculation of diameters of the largest included sphere, the largest free sphere and the largest included sphere along free sphere path
  • chan – (default: True) calculation of channel systems characterized by dimensionality as well as Di, Df and Dif
  • sa – (default: True) calculation of surface area accessible to a spherical probe, characterized by accessible surface area (ASA) and non-accessible surface area (NASA)
  • vol – (default: True) calculation of accessible volume (AV) and non-accessible volume (NAV)
  • volpo – (default: False) calculation of accessible probe-occupiable volume (POAV) and non-accessible probe-occupiable volume (PONAV)
  • psd – (default: True) calculation of the “derivative distribution” (change of AV w.r.t probe size) reported in the histogram file with 1000 bins of size of 0.1 Angstroem
  • 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