CITATION.cff

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cff-version: 1.2.0
title: pylimer-tools
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Tim
    family-names: Bernhard
    email: tim@bernhard.dev
    orcid: 'https://orcid.org/0009-0002-9227-0173'
identifiers:
  - type: doi
    value: 10.5281/zenodo.17582030
repository-code: 'https://github.com/GenieTim/pylimer-tools'
url: 'https://genietim.github.io/pylimer-tools/'
abstract: >-
  pylimer-tools is a collection of utility python functions
  for handling handling bead-spring polymers in Python.


  This toolbox provides an Monte Carlo (MC) structure
  generator, 

  simulation methods for Dissipative Particle Dynamics (DPD)
  with slip-springs,

  implementations of the Maximum Entropy Homogenization
  Procedure (MEHP), with and without slip-links,

  and various means to read LAMMPS output: be it data, dump
  or thermodynamic data files.

  Additionally, it provides various methods to calculate
  properties of the bead-spring networks, such as computing
  the radius of gyration, mean end to end distance, finding
  loops, or simply splitting a polymer network back up into
  its chains.
keywords:
  - polymer
  - Python
  - polymer networks
  - LAMMPS
license: GPL-3.0-or-later
preferred-citation:
    type: article
    authors:
      - family-names: Bernhard
        given-names: Tim
      - family-names: Gusev
        given-names: Andrei A.
      - family-names: Schwarz
        given-names: Fabian
    title: "pylimer-tools: A Python Package for Generating and Analyzing Bead-Spring Polymer Networks"
    doi: 10.5334/jors.609

references:
  - authors:
      - family-names: Miller
        given-names: Douglas R.
      - family-names: Macosko
        given-names: Christopher W.
    title: A New Derivation of Post Gel Properties of Network Polymers
    type: article
    doi: 10.1021/ma60050a004
    scope: >-
      Cite this paper if you used the Miller-Macosko Theory (MMT) to predict
      polymer properties
  - authors:
      - family-names: Macosko
        given-names: Christopher W.
      - family-names: Miller
        given-names: Douglas R.
    title: A New Derivation of Average Molecular Weights of Nonlinear Polymers
    type: article
    doi: 10.1021/ma60050a003
    scope: >-
      Cite this paper if you used the Miller-Macosko Theory (MMT) to predict
      polymer properties
  - authors:
      - family-names: Gusev
        given-names: Andrei A.
      - family-names: Bernhard
        given-names: Tim
    title: >-
      Molecular Model for Linear Viscoelastic Properties of Entangled Polymer
      Networks
    type: article
    doi: 10.1021/acs.macromol.4c01429
    scope: Cite this paper if you use the normal mode analysis of pylimer-tools
  - authors:
      - family-names: Gusev
        given-names: Andrei A.
    title: >-
      Numerical Estimates of the Topological Effects in the Elasticity of
      Gaussian Polymer Networks and Their Exact Theoretical Description
    type: article
    doi: 10.1021/acs.macromol.9b00262
    scope: >-
      Cite this paper if you use the Maximum Entropy Homogenization Procedure or
      the Monte-Carlo Universe Generator of pylimer-tools
  - authors:
      - family-names: Ramirez
        given-names: Jorge
      - family-names: Sukumaran
        given-names: Satihish K.
      - family-names: Vorselaars
        given-names: Bart
      - family-names: Likhtman
        given-names: Alexei E.
    title: >-
      Efficient on the Fly Calculation of Time Correlation Functions in Computer
      Simulations.
    type: article
    doi: 10.1063/1.3491098
    scope: Cite this paper if you used the multiple-tau autocorrelator
  - authors:
      - family-names: Schneider
        given-names: Jurek
      - family-names: Fleck
        given-names: Frank
      - family-names: Karimini-Varzaneh
        given-names: Hossein Ali
      - family-names: Müller-Plathe
        given-names: Florian
    title: Simulation of Elastomers by Slip-Spring Dissipative Particle Dynamics
    type: article
    doi: 10.1021/acs.macromol.1c00567
    scope: Cite this paper if you use our DPD simulator with slip-springs