Abstract
In this work, we describe the code structure, implementation, and usage of a Python-based, open-source framework, pyPRISM, for conducting polymer liquid-state theory calculations. Polymer Reference Interaction Site Model (PRISM) theory describes the equilibrium spatial-correlations, thermodynamics, and structure of liquid-like polymer systems and macromolecular materials. pyPRISM provides data structures, functions, and classes that streamline predictive PRISM calculations and can be extended for other tasks such as the coarse-graining of atomistic simulation force-fields or the modeling of experimental scattering data. The goal of providing this framework is to reduce the barrier to correctly and appropriately using PRISM theory and to provide a platform for rapid calculations of the structure and thermodynamics of polymeric fluids and polymer nanocomposites.
Highlights
Free and open-source (FOSS) scientific software lowers the barriers to applying theoretical techniques by codifying complex approaches into usable tools that can be leveraged by non-experts
[SC87] Despite the successful application of Polymer Reference Interaction Site Model (PRISM) theory to study a variety of complex soft-matter systems, [SC94] its use has been limited compared to other theory and simulation methods that have available open-source tools, such as Self-Consistent Field Theory (SCFT), [psc], [AQM+16] Molecular Dynamics (MD), [hoo], [GNA+15], [ALT08], [lam], [Pli95] or Monte Carlo (MC), [sim], [cas], [RM11]
Our previous publication, [MGIJ+18], focused primarily on the theoretical aspects of the method and presented several case studies to illustrate the utility of PRISM theory
Summary
Free and open-source (FOSS) scientific software lowers the barriers to applying theoretical techniques by codifying complex approaches into usable tools that can be leveraged by non-experts. The structure of these classes was kept as simple as possible so that novice scientific programmers could extend pyPRISM by implementing new closures, potentials, or intra-molecular correlation functions PyPRISM.MatrixArray objects can only contain numerical data and provide many operators and methods which simplify PRISM theory mathematics The former is necessary for carrying out the mathematics of the PRISM equation (Equation 1) and the latter for performing Fourier transformations of the individual pairfunctions. Classes which inherit from pyPRISM.Potential, pyPRISM.Closure, or pyPRISM.Omega represent interaction potentials, theoretical closures, or intra-molecular correla-
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