Automating embedded analysis capabilities and managing software complexity in multiphysics simulation part II: application to partial differential equations

A template-based generic programming approach was presented in a previous paper that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs). We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application

Parallel octree-based hexahedral mesh generation for eulerian to lagrangian conversion.

Computational simulation must often be performed on domains where materials are represented as scalar quantities or volume fractions at cell centers of an octree-based grid. Common examples include bio-medical, geotechnical or shock physics calculations where interface boundaries are represented only as discrete statistical approximations. In this work, we introduce new methods for generating Lagrangian computational meshes from Eulerian-based data. We focus specifically on shock physics problems that are relevant to ASC codes such as CTH and Alegra. New procedures for generating all-hexahedral finite element meshes from volume fraction data are introduced. A new primal-contouring approach is introduced for defining a geometric domain. New methods for refinement, node smoothing, resolving non-manifold conditions and defining geometry are also introduced as well as an extension of the algorithm to handle tetrahedral meshes. We also describe new scalable MPI-based implementations of these procedures. We describe a new software module, Sculptor, which has been developed for use as an embedded component of CTH. We also describe its interface and its use within the mesh generation code, CUBIT. Several examples are shown to illustrate the capabilities of Sculptor

Unconstrained Paving & Plastering: A New Idea for All Hexahedral Mesh Generation

Summary: Unconstrained Plastering is a new algorithm with the goal ofgenerating a conformal all-hexahedral mesh on any solid geometry assembly. Paving[1] has proven reliable for quadrilateral meshing on arbitrary surfaces. However, the 3D corollary, Plastering [2][3][4][5], is unable to resolve the unmeshed center voids due to being over-constrained by a pre-existing boundary mesh. Unconstrained Plastering attempts to leverage the benefits of Paving and Plastering, without the over-constrained nature of Plastering. Unconstrained Plastering uses advancing fronts to inwardly project unconstrained hexahedral layers from an unmeshed boundary. Only when three layers cross, is a hex element formed. Resolving the final voids is easier since closely spaced, randomly oriented quadrilaterals do not over-constrain the problem. Implementation has begun on Unconstrained Plastering, however, proof of its reliability is still forthcoming

An Approach to Combined Laplacian and Optimization-Based Smoothing for Triangular, Quadrilateral, and Quad-Dominant Meshes

Automatic finite element mesh generation techniques have become commonly used tools for the analysis of complex, real-world models. All of these methods can, however, create distorted and even unusable elements. Fortunately, several techniques exist which can take an existing mesh and improve its quality. Smoothing (also referred to as mesh relaxation) is one such method, which repositions nodal locations, so as to minimize element distortion. In this paper, an overall mesh smoothing scheme is presented for meshes consisting of triangular, quadrilateral, or mixed triangular and quadrilateral elements. This paper describes an efficient and robust combination of constrained Laplacian smoothing together with an optimization-based smoothing algorithm. The smoothing algorithms have been implemented in ANSYS and performance times are presented along with several example models

Engineered Repressible Lethality for Controlling the Pink Bollworm, a Lepidopteran Pest of Cotton

<div><p>The sterile insect technique (SIT) is an environmentally friendly method of pest control in which insects are mass-produced, irradiated and released to mate with wild counterparts. SIT has been used to control major pest insects including the pink bollworm (<em>Pectinophora gossypiella</em> Saunders), a global pest of cotton. Transgenic technology has the potential to overcome disadvantages associated with the SIT, such as the damaging effects of radiation on released insects. A method called RIDL (Release of Insects carrying a Dominant Lethal) is designed to circumvent the need to irradiate insects before release. Premature death of insects’ progeny can be engineered to provide an equivalent to sterilisation. Moreover, this trait can be suppressed by the provision of a dietary antidote. In the pink bollworm, we generated transformed strains using different DNA constructs, which showed moderate-to-100% engineered mortality. In permissive conditions, this effect was largely suppressed. Survival data on cotton in field cages indicated that field conditions increase the lethal effect. One strain, called OX3402C, showed highly penetrant and highly repressible lethality, and was tested on host plants where its larvae caused minimal damage before death. These results highlight a potentially valuable insecticide-free tool against pink bollworm, and indicate its potential for development in other lepidopteran pests.</p> </div

Fluorescent phenotypes of OX3347A and OX3402C.

<p>Photographs showing a wild-type pupa (left) and an OX3347A pupa (right) under (a) white light and (b) green fluorescent protein (ZsGreen) excitation wavelength light; and a wild-type pupa (left) and an OX3402C pupa (right) under (c) white light and (d) red fluorescent protein (DsRed2) excitation wavelength light.</p

Survival to adulthood of transgenic pink bollworm, heterozygous for an OX1124 insertion (line A, C, D or E), reared on larval diet with chlortetracycline (grey bars) or without chlortetracycline (white bars).

<p>Survival is expressed relative to that of each group’s wild-type siblings. Error bars indicate 95% confidence intervals.</p

Schematic representation of the RIDL cassette (markers and <i>piggyBac</i> sequences omitted) of constructs used for transformation of pink bollworm: (a) OX1124; (b) OX3347; (c) OX3400; and (d) OX3402.

<p>Schematic representation of the RIDL cassette (markers and <i>piggyBac</i> sequences omitted) of constructs used for transformation of pink bollworm: (a) OX1124; (b) OX3347; (c) OX3400; and (d) OX3402.</p