The main problem I always encounter with external packages or internal commands is that bonds that pass through the boundary of the simulation cell, or atoms that exist exactly at the wall of the cell(super common for inorganic structures, polymers, MOFS, coordination polymers, and all the interesting stuff...) always get problematic in some way. Bonds that pass through the wall usually break), other times atoms that exist on the wall get duplicated while they really shouldn't.
I have used topotools, Lammps-interface, Atomsk, OVITO and other external software with topotools and Lammps-interface seeming the most promising from a topological point of view, but again I get the same problems with them
How about a nonperiodic system (sphere) -- if it is possible with LAMMPS?
The problem with a MOF simulation (and other coordination polymers) is the periodicity. In theory, your system repeats the basic symmetric unit across all the space.
An approach could be identify the limit of your basic unit that reproduces the effect that you want to study/analyze. After you identify that limit (for example, using energetic or structural criteria), you could "cut" and "cap" the final bonds with appropriated real or virtual atoms (e.g. look at the truncation model used for a zeolite in this article:
https://www.sciencedirect.com/science/article/abs/pii/S2468823118306011
Dear Edward, I would prefer to somehow simulate the material as it is and not a capped version of it. I have managed to do this by connecting the disconnect atoms by changing manually the topology in the lammps data file but I find this so tiring and boring and even stupid maybe there should be a better solution... Lammps-interface manage to do this automaticly but the topology parameters must be refined in order to get all the angles and dihedrals right so the PXRD of the simulated material matches the PXRD of the real one. I find this exhausting and it gets catastrophicly complicated when you make big supercells. I am still trying to figure out how to solve this problems in an efficient way...
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