pysimm.apps.poreblazer

Module Contents

Functions

psd(s, **kwargs)

pysimm.apps.poreblazer.psd

surface(s, **kwargs)

pysimm.apps.poreblazer.surface

pore(s, **kwargs)

pysimm.apps.poreblazer.pore

void(s, **kwargs)

pysimm.apps.poreblazer.void

psd3(s, **kwargs)

pysimm.apps.poreblazer.psd3

Attributes

boltzmann_kcal

pysimm.apps.poreblazer.boltzmann_kcal = 0.001987204[source]
pysimm.apps.poreblazer.psd(s, **kwargs)[source]

pysimm.apps.poreblazer.psd

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]

pysimm.apps.poreblazer.surface

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.pore(s, **kwargs)[source]

pysimm.apps.poreblazer.pore

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.void(s, **kwargs)[source]

pysimm.apps.poreblazer.void

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

pysimm.apps.poreblazer.psd3(s, **kwargs)[source]

pysimm.apps.poreblazer.psd3

Perform combined pore volume, surface area, pore accessibility calculation using PoreBlazer v3.0 or later. For more detailed description of input parameters please check the Poreblazer GitHub page: https://github.com/SarkisovGroup/PoreBlazer

Parameters

  • atoms – file name to contain ff parameters (ff.atoms)

  • data – file name to write xyz file (data.xyz)

  • angles – angles of simulation box (90.0 90.0 90.0)

  • he_params – dictionary containing parameters for the helium atom probe: he_params[‘sigma’]: LJ sigma parameter [in Å] (2.58) he_params[‘eps’]: LJ epsilon parameter [in K] (10.22) he_params[‘temp’]: temperature [in K], required for the Helium porosimetry (300) he_params[‘cutoff’]: cut-off distance [in Å], required for the Helium porosimetry (12.0)

  • probe – nitrogen atom probe size [in Å] (3.314)

  • insertions – number of trials per atom for the surface area calculations (500)

  • probe_dr – linear size of a cell of the uniform grid [in Å] (0.2)

  • exec_path – full (relative or absolute) path to Poreblazer executable (poreblazer.exe)

Returns

0 if the Poreblazer finished successfully, and 1 otherwise

Return type

Exit status