Generation of finite element meshes on molecular surfaces

An increasingly important part of quantum chemistry involves molecular surfaces. To model such a surface, the basic idea is to assimilate each constituting atom with a simple sphere. Surface mesh generation techniques can then be used for visualization but also for simulation, where mesh quality has a strong influence on solution accuracy. This article presents a new approach to generating quality meshes on arbitrary molecular surfaces (van der Waals, solvent-accessible, or solvent-excluded surfaces). First, a boundary representation (B-rep) of the surface is obtained, i.e., a set of patches and the topological relations between them. Second, an appropriate parameterization is computed for each kind of patch and the user-specified element sizes are converted into an isotropic metric map. Third, meshes of the parametric domains are generated with respect to an induced anisotropic metric map, using a combined advancing-front-generalized Delaunay approach. Finally, these meshes are mapped onto the entire surface. The proposed method has been integrated within the BLMOL mesh generator and application examples are given to illustrate its capabilities. (C) 2003 Wiley Periodicals, Inc.