Molecular dynamics simulations of healing of a hole in a carbon nanotube under electron irradiation
Molecular dynamics simulations are performed to study healing of a hole in a carbon nanotube under electron irradiation in HRTEM at room temperature. The calculations are carried out using the CompuTEM algorithm as implemented in the MD-kMC code. Hole healing occurs in all the simulation runs. An amorphous patch is formed in the absence of external carbon adatoms only via saturation of dangling bonds. The patch consists of non-hexagonal rings, mostly of 5-, 6- and 7-membered rings, and its formation is accompanied by CNT buckling and narrowing. The amorphous patch growth is observed under further irradiation. Two-coordinated atoms play a leading role in this process.
Steps to reproduce
Folders rN contain to the data corresponding to continuation of 30 runs from the folder r(N-1). The files initialX.xyz contain the structures just after "successful" electron impacts, productX.xyz - during the structural relaxation after "successful" electron impacts and eqX.xyz - after structural relaxation and equilibration at 300 K. success.out contains the number and type of the atom knocked, transferred energy and estimated experimental time. 1atoms.out, 1rings.out contain statistics on different atom types and sizes of rings of the carbon bond network, respectively.