| 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.
Version information
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
Version 1.0: initial public release |
