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AMOrphous CHain builder: generate atomistic polymer chain structures
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README.md

amoch

AMOrphous CHain builder: create atomistic polymer chain structures

This simulator generates atomistic structures of amorphous systems using the continuous configurational bias Monte Carlo (CCBMC) method for adjusting torsion angles along the backbone of chain molecules while packing them into a cell.
AMOCH is an improved version of the builder that powers the PolymerModeler tool at nanoHUB.org.

chain

AMOCH makes heavy use of the OpenBabel project to support reading monomer molecules in many different file formats. The configure script attempts to identify OpenBabel libraries and header files on your system. If they are not found the build process will download and build a local copy of OpenBabel. You can pass --with-babel=dir to the configure script to identify an existing OpenBabel installation. You can also set the environment variables OPENBABEL_INCLUDE and OPENBABEL_LIB.

A few common polymers are defined in the data/ directory, along with standard Lennard-Jones interaction parameters. You can create similar files for monomers and parameters that you use often.

This code is distributed under the GNU General Public License (GPL), version 3. The SIMD Fast Mersenne Twister (SFMT) library (see lib/SFMT) is distributed under the terms specified in lib/SFMT/LICENSE.txt.

See here for documentation of the input file format.

Build

./configure [--with-babel=<dir>|build] [--enable-float]
make
make test

Workflow

The wf/ directory contains JSON and Python files to support using AMOCH in an iterative amorphous system building workflow, using the Workflow library.

By default AMOCH will build the entire atomistic system, which can then be converted to, say, a LAMMPS input file and relaxed. Experience has shown that occasionally the CCBMC builder will get trapped in a high energy region of the energy landscape represented by the torsion angles of all the chains in a system, and the resulting system is incredibly difficult to relax before pursuing MD studies of mechanical properties. By using an iterative workflow, we can relax the system in stages as it is built. The workflow looks like this:

  • Run AMOCH to add a few new monomers to the system
  • Assign atom types to the atoms in the system based on connectivity
  • Generate a LAMMPS data file
  • Run LAMMPS to minimize energy interactions

The force field typer in the wf/ directory assigns Dreiding atom types.

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