Polymatic is a set of codes for structure generation of amorphous polymers by a simulated polymerization algorithm. The main task of Polymatic is to perform polymerization steps within a system based on a number of defined bonding criteria. It works in conjunction with a simulation package to perform energy minimization and molecular dynamics simulations during the polymerization.
Currently, Polymatic is written to work with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) with a class I or class II force field. However, the majority of the subroutines in the code do not rely on using LAMMPS or these force field definitions, such that the code could be easily extended to work with other force fields, file types, and software packages.
New for version 1.1 (August 16, 2015):
- Polymatic.pm perl module with subroutines for reading and writing various file types
- Python script to handle the algorithm workflow
- Support for class I and class II force fields
- Random packing into an existing structure
- Updated intramolecular bonding criteria and alignment criteria
The development of Polymatic was supported in part by funding from the National Science Foundation (NSF) through grant DMR-0908781. Additionally, computational resources and support were provided by the Research Computing and Cyberinfrastructure unit of Penn State Information Technology Services and the Materials Simulation Center of the Materials Research Institute.
The following paper describes the basic Polymatic algorithm and its implementation for a variety of linear polymers. If you publish work using the Polymatic code or variations of it, please cite this paper along with the source code. Abbott, L. J.; Hart, K. E.; Colina, C. M. "Polymatic: A generalized simulated polymerization algorithm for amorphous polymers." Theoretical Chemistry Accounts, 2013, 132, 1334. DOI: 10.1007/s00214-013-1334-z (http://dx.doi.org/10.1007/s00214-013-1334-z)
Cite this work
Researchers should cite this work as follows:
- polymer builder
- structure generation
- molecular simulation
- simulated polymerization
- virtual synthesis
- molecular dynamics
- Amorphous Materials