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A python tool for Polymer Reference Interaction Site Model (PRISM) calculations

Project description

pyPRISM

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Polymer Reference Interaction Site Model (PRISM) theory describes the equilibrium spatial-correlations of liquid-like polymer systems including melts, blends, solutions, block copolymers, ionomers, liquid crystal forming polymers and nanocomposites. Using PRISM theory, one can calculate thermodynamic (e.g., second virial coefficients, Flory-Huggins interaction parameters, potentials of mean force) and structural (eg., pair correlation functions, structure factors) information for these macromolecular materials. pyPRISM is a Python-based, open-source framework for conducting PRISM theory calculations. This framework aims to simplify PRISM-based studies by providing a user-friendly scripting interface for setting up and numerically solving the PRISM equations. pyPRISM also provides data structures, functions, and classes that streamline PRISM calculations, allowing pyPRISM to be extended for use in other tasks such as the coarse-graining of atomistic simulation force-fields or the modeling of experimental scattering data. The goal of 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 nanocomposites.

Citation

If you use pyPRISM in your work, we ask that you please cite both of the following articles

  1. Martin, T.B.; Gartner, T.E III; Jones, R.L.; Snyder, C.R.; Jayaraman, A.; pyPRISM: A Computational Tool for Liquid State Theory Calculations of Macromolecular Materials, Macromolecules, 2018, 51 (8), p2906-2922 link

  2. Schweizer, K.S.; Curro, J.G.; Integral Equation Theory of the Structure of Polymer Melts, Physical Review Letters, 1987, 58 (3) p246-249 link

Example

Below is an example python script where we use pyPRISM to calculate the pair correlation functions for a nanocomposite (polymer + particle) system with attractive polymer-particle interactions. Below the script is a plot of the pair correlation functions from this calculation. See here for a more detailed discussion of this example.

import pyPRISM

sys = pyPRISM.System(['particle','polymer'],kT=1.0)
sys.domain = pyPRISM.Domain(dr=0.01,length=4096)
    
sys.density['polymer']  = 0.75
sys.density['particle'] = 6e-6

sys.diameter['polymer']  = 1.0
sys.diameter['particle'] = 5.0

sys.omega['polymer','polymer']   = pyPRISM.omega.FreelyJointedChain(length=100,l=4.0/3.0)
sys.omega['polymer','particle']  = pyPRISM.omega.InterMolecular()
sys.omega['particle','particle'] = pyPRISM.omega.SingleSite()

sys.potential['polymer','polymer']   = pyPRISM.potential.HardSphere()
sys.potential['polymer','particle']  = pyPRISM.potential.Exponential(alpha=0.5,epsilon=1.0)
sys.potential['particle','particle'] = pyPRISM.potential.HardSphere()

sys.closure['polymer','polymer']   = pyPRISM.closure.PercusYevick()
sys.closure['polymer','particle']  = pyPRISM.closure.PercusYevick()
sys.closure['particle','particle'] = pyPRISM.closure.HyperNettedChain()

PRISM = sys.solve()

pcf = pyPRISM.calculate.prism.pair_correlation(PRISM)

Quick Install

The commands below should install pyPRISM with all basic dependences via conda or pip. These commands should be platform agnostic and work for Linux, macOS, and Windows if you have Anaconda or pip installed. For full installation instructions please see the documentation.

$ conda install -c conda-forge pyPRISM

or

$ pip install pyPRISM

Documentation

Code documentation is hosted on pyprism.readthedocs.io. The most up to date code documentation can always be found by compiling from source.

Contact Us

Please use the Issue tracker to submit questions or suggestions for the project. For other correspondence, please contact one of the team-members below.

Legal

NIST Disclaimer

Any identification of commercial or open-source software in this document is done so purely in order to specify the methodology adequately. Such identification is not intended to imply recommendation or endorsement by the National Institute of Standards and Technology, nor is it intended to imply that the softwares identified are necessarily the best available for the purpose.

NIST License

This software was developed by employees of the National Institute of Standards and Technology (NIST), an agency of the Federal Government and is being made available as a public service. Pursuant to title 17 United States Code Section 105, works of NIST employees are not subject to copyright protection in the United States. This software may be subject to foreign copyright. Permission in the United States and in foreign countries, to the extent that NIST may hold copyright, to use, copy, modify, create derivative works, and distribute this software and its documentation without fee is hereby granted on a non-exclusive basis, provided that this notice and disclaimer of warranty appears in all copies.

THE SOFTWARE IS PROVIDED 'AS IS' WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND FREEDOM FROM INFRINGEMENT, AND ANY WARRANTY THAT THE DOCUMENTATION WILL CONFORM TO THE SOFTWARE, OR ANY WARRANTY THAT THE SOFTWARE WILL BE ERROR FREE. IN NO EVENT SHALL NIST BE LIABLE FOR ANY DAMAGES, INCLUDING, BUT NOT LIMITED TO, DIRECT, INDIRECT, SPECIAL OR CONSEQUENTIAL DAMAGES, ARISING OUT OF, RESULTING FROM, OR IN ANY WAY CONNECTED WITH THIS SOFTWARE, WHETHER OR NOT BASED UPON WARRANTY, CONTRACT, TORT, OR OTHERWISE, WHETHER OR NOT INJURY WAS SUSTAINED BY PERSONS OR PROPERTY OR OTHERWISE, AND WHETHER OR NOT LOSS WAS SUSTAINED FROM, OR AROSE OUT OF THE RESULTS OF, OR USE OF, THE SOFTWARE OR SERVICES PROVIDED HEREUNDER.

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