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
- Grayce, Schweizer, Solvation potentials for macromolecules, J. Chem. Phys., 1994 100 (9) 6846 [link]
- 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']