Theory · 1 methods
Packing
What CAPS computes, as it computes it: the equation, its symbols with CAPS's defaults, when to use the method, the source file, the tests that check it, and any departure from the cited method.
Overlap-penalty packing
Molecules are rigid bodies (centre and rotation). A smooth penalty for atoms of different molecules closer than the tolerance, plus penalties for leaving their regions, is minimised with L-BFGS; the worst-placed molecules are moved between rounds.
$$f = \sum_{i<j,\ \text{different molecules}} \max\left(0,\; d^2 - |x_i - x_j|^2\right)^2 + w\sum_i g_\text{region}(x_i)^2$$
Martínez et al. 2009 (the Packmol objective)
| Symbol | Meaning | In CAPS |
|---|---|---|
| d | tolerance | 2.0 Å |
| w | region weight | — |
| rounds | optimisation rounds | 60 × 400 L-BFGS iterations |
When to use it
Solvents, fluids in pores, curatives inserted into a cell, mixtures from packmol input files.
- Source
core/src/pack.cpp- Tested by
- Pack.PeriodicWaterBoxMeetsTolerance · Pack.RegionsAndFixedMolecules · Pack.SameSeedSamePacking
- Departure from the reference
- none
References
- Martínez, L., Andrade, R., Birgin, E. G., Martínez, J. M., "PACKMOL: a package for building initial configurations for molecular dynamics simulations", J. Comput. Chem. 30, 2157–2164 (2009). doi:10.1002/jcc.21224
- Liu, D. C., Nocedal, J., "On the limited memory BFGS method for large scale optimization", Math. Program. 45, 503–528 (1989). doi:10.1007/BF01589116