01_Introduction

1.1 About Ambuild

The Amorphous Builder (Ambuild) code is a program designed to simulate the conditions under which amorphous hyper-crosslinked polymers are formed, building the polymer network up from the molecular building blocks themselves (Figure 1).

Ambuild is written in Python and integrates to HOOMD-blue (Figure 2), a Graphics Processing Unit (GPU) -based molecular dynamics (MD) code also written in Python. (HOOMD-blue can be accessed via: http://codeblue.umich.edu/hoomd-blue). The integration of the Ambuild code with HOOMD-blue enables very large simulation cell sizes to be used, whilst retaining precise control of the simulation cell contents and structure generation process.

1.2 Concepts

Ambuild works with cells, fragments, building blocks, and endGroups:

• The cell is a volume of space that will be filled with molecular

building blocks.

• Fragments are molecules that may contain one or more endGroups that

can be used to form bonds. Fragments are always contained within building blocks.

• A building block may house one or more fragments of the same or

different types. The fragments within a building block are bonded to each other via their endGroups, the atoms which will form part of the new bond between building blocks. Rules can be specified for which endGroups can bond to which others, the dihedral angle around the bond that the fragment should adopt, and any atoms that may need to be removed on bonding, such as occurs during an unsaturation process.