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Prototype2009: Bond Formation

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The bond formation code currently in place is primitive. It met the requirement of having bonds be able to form during simulation time and effect the result of the simulation from that point. These requirements allowed us to have working data for developing the other parts of the system. It is our intention to replace this with GROMACS QM, and have bonds be an emergent property from the QM.

The bonds are formed based on the distance between atoms. The maximum distance for atom bonding is specified in the simulation specification. This specification applies to all atom types.

The current algorithm used for bond formation is such:

  1. For each atom, find neighbors within the bonding range.
  2. If already bonded, Done.
  3. If both atoms have less then 4 bonds, form a bond. Done.
  4. For each atom, test the separation distance for their existing bonds against the current potential bond. Remove the largest separation bond that is larger then the potential bond.
  5. Form the bond.
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