Polymer Modeler

By Benjamin P Haley1; Nate Wilson1; Chunyu Li1; Andrea Arguelles; Eugenio Jaramillo; Alejandro Strachan1

1. Purdue University

Build thermoplastic polymer chains and run LAMMPS to relax the chains and study mechanical properties

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Version 3.41 - published on 03 Jun 2022

doi:10.21981/E95G-BP68 cite this

This tool is closed source.

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    Pre-built epoxy structure Specify monomer(s) used to build chains Specify molecular dynamics simulation options Download resulting LAMMPS input files Output plot of energy over time Isotactic freely rotating PMMA chain with simulation cell Animation of torsion angle rotation in polyethylene

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Tools

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Abstract

This tool provides a chain builder, with options to specify monomers, monomer arrangements (tacticity), torsion angles between monomers, system parameters such as density and temperature, as well as some prebuilt epoxy structures from current research interests. The resulting structure (constructed or prebuilt) can be used as input to LAMMPS to run molecular dynamics (MD) simulations. Many MD options are available.  Structures packed with this tool may be used as inputs to the nuSIMM tool.

 

Version information

Version 3.38

  • Fixed a bug in the builder that caused exponential slowdown for monomers with large side groups (>30 atoms)

Version 3.37

  • Fixed a bug with uploaded zmatrices that ignored the length of the backbone

Version 3.36

  • Fixed a bug in torsion rotation for certain internal coordinate conditions
  • Changed format of LAMMPS dump file to use unwrapped coordinates

Version 3.35 

  • Added prebuilt polyethylene structures

Version 3.34

  • Added tacticity options for polypropylene 

Version 3.33

  • Fixed problems with thermalizing prebuilt structures
  • Updated trajectory animations to use unwrapped coordinates
  • Added support for Si to the builder
  • Fixed a bug that generated nvt/sllod fixes for LAMMPS for non-deforming systems

Version 3.32

  • Expanded field labels for better integration with tgnb tool

Version 3.31

  • Code cleanup

Version 3.30

  • Fixed a bug in Polymatic/nuSIMM input file generation

Version 3.29

  • Added extra error handling to give more debugging information in the event of a LAMMPS crash

Version 3.28

  • Added volume and density to the thermodynamic outputs of LAMMPS
  • Added initial velocities for MD steps after structural relaxation
  • Updated to LAMMPS version 15May15
  • Removed fixed 600K thermalization temperature; use MD temperature to thermalize 

Version 3.27

  • Fixed a bug that caused crashes when running multiple simulations in a tool session

Version 3.25, 3.26

  • ReaxFF bug fixes

Version 3.24

  • Added support for ReaxFF data files

Version 3.23

  • Fixed errors in improper angle generation for LAMMPS data file

Version 3.20, 3.21, 3.22

  • Fixed errors in PMMA monomer zmatrices

New in version 3.19

  • Corrected problems in atactic PMMA generation for nuSIMM

New in version 3.18

  • Bug fixes in generating input files for nuSIMM
  • By default, only torsions between monomers rotate when configuring chains using CBMC method, rather than internal torsions along the backbone.  Internal torsion rotation can be enabled.

New in version 3.17

  • Improved handling for resonant types other than C;  improved handling of unidentified atom types in LAMMPS parameter generation

New in versions 3.15 and 3.16

  • Minor bug fixes

 

New in version 3.14

  • Fixed bug in LAMMPS pair_coeff generation

 

New in version 3.13

  • Fixed bug in generation of Polymatic inputs with no improper angles

 

New in version 3.12

  • LAMMPS data file created as an input to the Polymatic tool now includes pair coefficients.

 

New in versions 3.10 and 3.11

  • Minor bug fixes

 

New in version 3.9

  • Added bead monomer to list of available monomers


New in version 3.8

  • Fixed bugs in handling of custom torsions
  • Improved generation of internal coordinates from PDB input


New features in version 3.7

  • Fixed a bug in the builder that prevented modeling monomers as beads


New features in version 3.6

  • Bug fix for LAMMPS executable path on nanoHUB


New features in version 3.5

  • Bug fix for dihedral style in prebuilt EPON862 systems

 


New features in version 3.4

 

  • Bug fix for rodlike polymers


New features in version 3.3

  • Improved sampling of torsion space
  • New option to minimize built structure using an n-step push off in the spirit of the method described by Auhl et al. in J. Chem. Phys 119, 12718 (2003)
  • Improved error handling to provide better error messages if LAMMPS crashes
  • Updated parallel LAMMPS to 4Jul12 release
  • Submit polymer building runs over 10,000 atoms to HPC resources; previously this ran in the nanoHUB container and would often encounter time and memory limits
  • Bug fixes


New features in versions 3.1 and 3.2

  • Fixed bugs in LAMMPS Dreiding parameter generation


New features in version 3.0

  • Upload monomers in PDB and XYZ format, rather than z-matrix
  • Upload LAMMPS data file (and pair coefficients) from previous LAMMPS run as initial structure, for restarting or continuing mechanical property simulation
  • Simplified structure and configuration inputs


New features in version 2.3

  • Fixed electrostatic-pair_style conflict bug in generated LAMMPS input file


New features in version 2.2

 

  • LAMMPS failures result in an error message in the output log, rather than stack traces dumped to the screen.
  • Correct setup of LAMMPS input file for systems with no impropers


New features in version 2.1

 

 

  • Gasteiger charge calculation
  • Correct handling of bonds not explicitly specified by input z-matrix: missing bonds added. This fixes the problem addressed by this question
  • Submission of large builds to HPC resources
  • Distinction between isotactic, syndiotactic, and atactic polystyrene
  • Automatic grid spacing determined from self-avoiding or Lennard-Jones cutoffs
  • Bonded (covalent) torsion energies included along with non-bonded Lennard-Jones energies in Monte Carlo sampling
  • Updated PMMA z-matrix
  • Bug fixes, including the resolution of this question


New features in version 2.0

 

 

  • Significant speed increase (~10x) in building chains
  • Specify multiple monomers and arrangements of monomers for e.g. isotactic, syndiotactic, and atactic chains
  • Specify which torsion angles along the backbone of a chain are permitted to rotate and energies or probabilities of each configuration
  • Improved self-avoiding algorithm
  • Long range Lennard-Jones interactions between chain atoms separated by more than 4 bonds and interactions between chains
  • Chain length histogram
  • Global energy minimization before running MD, which fixes several outstanding problems, including this question, this question, and this ticket
  • Plot density vs time during MD simulations
  • Trajectory animation, in response to this wish


New features in version 1.4

 

 

  • Bug fixes for LAMMPS input file generation


New features in version 1.3

 

 

  • New self-avoiding algorithm in the chain builder (this is still a work-in-progress)
  • Parallel LAMMPS simulations
  • Download generated LAMMPS input files: script (commands) and data files, granting this wish
  • Added new pre-built systems: EPON 862 in various stages of cross linking
  • Reorganized and expanded strain options


New features in version 1.2

 

 

  • Added self-avoiding algorithm to the chain builder
  • Fixed output units on energy and stress plots
  • Added progress bar for LAMMPS simulations of pre-built structures


New features in version 1.1

 

 

  • Minor bugfixes


Version 1.0: initial public release

 

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Chain building powered by PolymerBuilder by Benjamin P. Haley MD simulations powered by LAMMPS

Sponsored by

Cyber-enabling polymer research tools supported by the National Science Foundation (NSF).

Cite this work

Researchers should cite this work as follows:

  • Benjamin P Haley, Nate Wilson, Chunyu Li, Andrea Arguelles, Eugenio Jaramillo, Alejandro Strachan (2022), "Polymer Modeler," https://nanohub.org/resources/polymod. (DOI: 10.21981/E95G-BP68).

    BibTex | EndNote

Tags

  1. Amorphous Materials
  2. computational materials science
  3. LAMMPS
  4. materials science
  5. molecular dynamics (MD)
  6. nano/bio
  7. NCN Group - Materials Science
  8. Polymer Modeler
  9. polymers
  10. Simulation