pyPRISM.calculate.solvation_potential module

pyPRISM.calculate.solvation_potential.solvation_potential(PRISM, closure='HNC')[source]

Calculate the pairwise decomposed medium-induced solvation potential

Parameters:
  • PRISM (pyPRISM.core.PRISM) – A solved PRISM object.
  • closure (str ('PY' or 'HNC')) – closure used to derive the potential
Returns:

psi – MatrixArray of the Real-space solvation potentials
Return type:

pyPRISM.core.MatrixArray

Mathematical Definition

\[\text{PY: } \Delta \hat{\Psi}^{PY}(k) = - k_B T \ln(1 + \hat{C}(k)\hat{S}(k)\hat{C}(k))\]
\[\text{HNC: } \Delta \hat{\Psi}^{HNC}(k) = - k_B T \hat{C}(k)\hat{S}(k)\hat{C}(k)\]

Variable Definitions

  • \(\Delta \hat{\Psi}^{PY}\), \(\Delta \hat{\Psi}^{HNC}\)
    Percus-Yevick and Hypernetted Chain derived pairwise decomposed solvation potentials, each described as a MatrixArray. This implies that the multiplication in the above equation is actually matrix multiplication and the individual solvation potentials are extracted as pair-functions of the MatrixArrays. Note that the solvation potential MatrixArrays are inverted back to Real-space for use.
  • \(\hat{C}(k)\)
    Direct correlation function MatrixArray at a wavenumber \(k\)
  • \(\hat{S}(k)\)
    Structure factor MatrixArray at a wavenumber \(k\)
  • \(k_B T\)
    Thermal temperature written as the product of the Boltzmann constant and temperature.

Description

The solvation potential (\(\Delta \hat{\Psi}\)) mathematically describes how a given surrounding medium perturbs the site-site pairwise interactions of a molecule.

This calculation is the foundation of the Self-Consistent PRISM formalism. See Self-Consistent PRISM Method for more information.

Warning

Passing an unsolved PRISM object to this function will still produce output based on the default values of the attributes of the PRISM object.

References

  1. Grayce, Schweizer, Solvation potentials for macromolecules, J. Chem. Phys., 1994 100 (9) 6846 [link]
  2. Schweizer, Honnell, Curro, Reference interaction site model theory of polymeric liquids: Self-consistent formulation and nonideality effects in dense solutions and melts, J. Chem. Phys., 1992 96 (4) 3211 [link]

Example

import pyPRISM

sys = pyPRISM.System(['A','B'])

# ** populate system variables **

PRISM = sys.createPRISM()

PRISM.solve()

psi = pyPRISM.calculate.solvation_potential(PRISM)

psi_BB = psi['B','B']