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Non-equilibrium molecular dynamics simulations are performed to investigate how changing the number of structural defects in the wall of a (7,7) single-walled carbon nanotube (CNT) affects water transport and internal fluid dynamics. Structural defects are modelled as vacancy sites (missing carbon atoms). We find that, while fluid flow rates exceed continuum expectations, increasing numbers of defects lead to significant reductions in fluid velocity and mass flow rate. The inclusion of such defects causes a reduction in the water density inside the nanotubes and disrupts the nearly frictionless water transport commonly attributed to CNTs. [ABSTRACT FROM PUBLISHER]

A computational pre-processing tool for generating initial configurations of molecules for molecular dynamics simulations in geometries described by a mesh of unstructured arbitrary polyhedra is described. The mesh is divided into separate zones and each can be filled with a single crystal lattice of atoms. Each zone is filled by creating an expanding cube of crystal unit cells, initiated from an anchor point for the lattice. Each unit cell places the appropriate atoms for the user-specified crystal structure and orientation. The cube expands until the entire zone is filled with the lattice; zones with concave and disconnected volumes may be filled. When the mesh is spatially decomposed into portions for distributed parallel processing, each portion may be filled independently, meaning that the entire molecular system never needs to fit onto a single processor, allowing very large systems to be created. The computational time required to fill a zone with molecules scales linearly with the number of cells in the zone for a fixed number of molecules, and better than linearly with the number of molecules for a fixed number of mesh cells. Our tool, molConfig, has been implemented in the open source C++ code OpenFOAM. [ABSTRACT FROM AUTHOR]