SANDBOX input and output

The SANDBOX keyword requires an auxiliary input file rbdata and produces an output visualization file The coords file is read in the normal angle-axis fashion: for $ N$ rigid bodies, the first $ N$ lines are positions and the second $ N$ lines are the corresponding angle-axis rotations.

The SANDBOX potential generates a unary or $ n$-ary mixture of rigid bodies (``molecules'') composed of sites. Each site has a molecule-frame position and orientation. The orientation in the molecule frame is specified by an angle-axis rotation. Each site also has an interaction class that specifies how it interacts with sites in other molecules. These interactions are specified in an interaction matrix. A site of interaction class $ i$ interacts with a site of interaction class $ j$ according to the $ (i,j)$-th element of the interaction matrix. This element of the matrix specifies a potential (e.g., LJ, dipole, etc.) and the appropriate parameters (e.g., energy and length scales, dipole strength, etc.).


David Wales 2018-06-21