pysimm.apps.poreblazer module

pysimm.apps.poreblazer.pore(s, **kwargs)[source]

Perform pore volume calculation using PoreBlazer v2.0

Parameters:
  • atoms – file name to contain ff parameters (ff.atoms)
  • data – file name to write xyz file (data.xyz)
  • angles – angles of simlation box (90.0 90.0 90.0)
  • insertions – number of insertions for calculation (1000)
  • temp – temperature at which to perform simulation (300)
  • pore_probe – sigma, epsilon, cutoff parameters for probe (2.58, 10.22, 12.8)
  • exec_path – path to poreblazer pore executable (pore_he.exe)
Returns:

None
pysimm.apps.poreblazer.psd(s, **kwargs)[source]

Perform pore size distribution calculation using PoreBlazer v2.0

Parameters:
  • atoms – file name to contain ff parameters (ff.atoms)
  • data – file name to write xyz file (data.xyz)
  • angles – angles of simlation box (90.0 90.0 90.0)
  • insertions – number of insertions for calculation (500)
  • min_probe – minimum probe size (1.0)
  • probe_dr – step size to increase probe size (0.2)
  • max_probe – maximum probe size: 25
  • psd_save – T/F to save psd points (F)
  • psd_range – range in which to save psd points (2.5,3.8)
  • exec_path – path to poreblazer psd executable (psd.exe)
  • gen_files – if True, only generate input do not execute (None)
Returns:

None
pysimm.apps.poreblazer.surface(s, **kwargs)[source]

Perform accessible surface area calculation using PoreBlazer v2.0

Parameters:
  • atoms – file name to contain ff parameters (ff.atoms)
  • data – file name to write xyz file (data.xyz)
  • angles – angles of simlation box (90.0 90.0 90.0)
  • insertions – number of insertions for calculation (1000)
  • probe – probe size (3.681)
  • probe_type – type of probe (hs)
  • vis – True to save visual (F)
  • exec_path – path to poreblazer surface executable (surface.exe)
Returns:

None
pysimm.apps.poreblazer.void(s, **kwargs)[source]

Perform pore volume calculation using PoreBlazer v2.0 assuming a probe size of 0 to calculate void volume

Parameters:
  • atoms – file name to contain ff parameters (ff.atoms)
  • data – file name to write xyz file (data.xyz)
  • angles – angles of simlation box (90.0 90.0 90.0)
  • insertions – number of insertions for calculation (1000)
  • temp – temperature at which to perform simulation (300)
  • pore_probe – sigma, epsilon, cutoff parameters for probe (0.00, 10.22, 12.8)
  • exec_path – path to poreblazer pore executable (pore_he.exe)
Returns:

None