dfemtoolz: An open-source C++ framework for efficient imposition of material and boundary conditions in finite element biomedical simulations

Abstract

© 2019 Elsevier B.V. We propose a novel C++ open-source package dfemtoolz that enables highly efficient: (1) discretization of a triangular surface mesh into volumetric tetrahedral elements (by using the Tetgen); (2) splitting of prism or tetrahedral meshes into hexahedral meshes; and (3) application of boundary conditions for modeling various physical phenomena (i.e. fluid flow, structural analysis, heat transfer, mass transport, etc.). The novelty of the proposed library is two-fold: (1) it avoids computationally expensive merging by performing a more efficient search of neighboring nodes; and (2) it enables highly efficient manipulation of nodes’ BCs in the bitwise manner. The framework is initially proposed and validated for biomedical simulations; however, it could have wide-scale applications. Program summary: Program Title: dfemtoolz Program Files doi: http://dx.doi.org/10.17632/9xy4x3ggch.1 Licensing provisions: GNU General Public License 3 Programming language: C++ Nature of the problem: In silico trials assume reproducing medical phenomena on computers with the aim to reduce harms, costs and time required for performing traditional clinical trials. A typical in silico workflow consists of the following six steps: (1) Segmentation of medical scans; (2) Reconstruction of the segmented region; (3) Meshing of the obtained volume; (4) Application of appropriate materials and boundary conditions (BCs); (5) Solving governing equations that describe how the considered phenomena will behave under the specified conditions and (6) Visualization of the obtained results. At the moment, there are available mature open-source frameworks for solving the following tasks: segmentation (i.e. ITK, ImageJ), meshing (i.e. Tetgen, Triangle), simulation (i.e. OpenFOAM, Elmer, FEniCS) and visualization (i.e. VTK, OpenGL). However, the step 4 (application of materials and boundary conditions) remains an open question in terms of open-source packages. To the best of our knowledge, there is no robust and publically available framework for these purposes – which inspired us to propose the dfemtoolz with the aim to improve compatibility and ease integration of the overall six in silico trials steps. Solution method: The dfemtoolz is provided as both stand-alone executable modules and C++ library that could be integrated into an existing software package. The dfemtoolz supports two use-case scenarios: (1) a user has a surface geometry of the FEM model that needs to be discretized before further application of boundary conditions; and (2) a user has an existing FE mesh and only needs to prescribe BCs. Since it is generic, the dfemtoolz is capable of processing any FEM model represented as a list of nodes (defined with coordinates in an arbitrary dimension) and a list of elements (of an arbitrary type). Additional comments: The source code, working examples and benchmarks are available for download at the URL: https://github.com/dmilashinovic/dfemtoolz and are tested to work under Linux and Windows OS. The library was developed using the Code