David A. Ham
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View article: Missing Physics Discovery through Fully Differentiable Finite Element-Based Machine Learning
Missing Physics Discovery through Fully Differentiable Finite Element-Based Machine Learning Open
Although many problems in science and engineering are modelled by well-established PDEs, they often involve unknown or incomplete relationships, such as material constitutive laws or thermal response, that limit accuracy and generality. Ex…
View article: Automating the construction of time-parallel 4DVar data assimilation systems for finite element models.
Automating the construction of time-parallel 4DVar data assimilation systems for finite element models. Open
Data assimilation (DA) has made a significant contribution to the increase in forecast skill in recent decades by leveraging real-world observations to improve the states used in the forecasting system. However, the DA stage comprises a la…
View article: Constructing PDFs of spatially dependent fields using finite elements
Constructing PDFs of spatially dependent fields using finite elements Open
A probability density function (PDF) of a spatially dependent field provides a means of calculating moments of the field or, equivalently, the proportion of a spatial domain that is mapped to a given set of values. This paper describes a f…
View article: Differentiable programming across the PDE and Machine Learning barrier
Differentiable programming across the PDE and Machine Learning barrier Open
The combination of machine learning and physical laws has shown immense potential for solving scientific problems driven by partial differential equations (PDEs) with the promise of fast inference, zero-shot generalisation, and the ability…
View article: Consistent point data assimilation in Firedrake and Icepack
Consistent point data assimilation in Firedrake and Icepack Open
We present a high-level, differentiable, and composable abstraction for the point evaluation of the solution fields of partial differential equation models. The new functionality, embedded in the Firedrake automated finite element system, …
View article: Automatic adjoint-based inversion schemes for geodynamics: reconstructing the evolution of Earth's mantle in space and time
Automatic adjoint-based inversion schemes for geodynamics: reconstructing the evolution of Earth's mantle in space and time Open
Reconstructing the thermo-chemical evolution of Earth's mantle and its diverse surface manifestations is a widely recognised grand challenge for the geosciences. It requires the creation of a digital twin: a digital representation of Earth…
View article: checkpoint_schedules: schedules for incrementalcheckpointing of adjoint simulations
checkpoint_schedules: schedules for incrementalcheckpointing of adjoint simulations Open
International audience
View article: Efficient N-to-M Checkpointing Algorithm for Finite Element Simulations
Efficient N-to-M Checkpointing Algorithm for Finite Element Simulations Open
In this work, we introduce a new algorithm for N-to-M checkpointing in finite element simulations. This new algorithm allows efficient saving/loading of functions representing physical quantities associated with the mesh representing the p…
View article: Automatic adjoint-based inversion schemes for geodynamics: Reconstructing the evolution of Earth’s mantle in space and time
Automatic adjoint-based inversion schemes for geodynamics: Reconstructing the evolution of Earth’s mantle in space and time Open
Reconstructing the thermo-chemical evolution of Earth's mantle and its diverse surface manifestations is a widely-recognised grand challenge for the geosciences. It requires the creation of a digital twin: a digital representation of Earth…
View article: Absorbing boundary conditions for the Helmholtz equation using Gauss-Legendre quadrature reduced integrations
Absorbing boundary conditions for the Helmholtz equation using Gauss-Legendre quadrature reduced integrations Open
We introduce a new class of absorbing boundary conditions (ABCs) for the Helmholtz equation. The proposed ABCs are obtained by using $L$ discrete layers and the $Q_N$ Lagrange finite element in conjunction with the $N$-point Gauss-Legendre…
View article: Consistent Point Data Assimilation in Firedrake and Icepack
Consistent Point Data Assimilation in Firedrake and Icepack Open
When estimating quantities and fields that are difficult to measure directly, such as the fluidity of ice, from point data sources, such as satellite altimetry, it is important to solve a numerical inverse problem that is formulated with B…
View article: Physics-driven machine learning models coupling PyTorch and Firedrake
Physics-driven machine learning models coupling PyTorch and Firedrake Open
Partial differential equations (PDEs) are central to describing and modelling complex physical systems that arise in many disciplines across science and engineering. However, in many realistic applications PDE modelling provides an incompl…
View article: Point Data Assimilation in Firedrake and Icepack
Point Data Assimilation in Firedrake and Icepack Open
We present methods and tools which significantly improve the ability to estimate quantities and fields which are difficult to directly measure at large scales, such as the fluidity of ice, using point data sources from remote sensing. Our …
View article: Comment on gmd-2022-239
Comment on gmd-2022-239 Open
Abstract. Mitigating diffuse-source nutrient pollution has created an urgent need to advance understanding of catchment hydrological and nutrient dynamics, and develop robust integrated hydrological and water quality models to support deci…
View article: Reply on AC1
Reply on AC1 Open
Abstract. Lagrangian particle tracking schemes allow a wide range of flow and transport processes to be simulated accurately, but a major challenge is numerically implementing the inter-particle interactions in an efficient manner. This ar…
View article: Comment on gmd-2022-180
Comment on gmd-2022-180 Open
Abstract. Volcanoes are a known source of halogens to the atmosphere. HBr volcanic emissions lead rapidly to the formation of BrO within volcanic plumes. BrO, having a longer residence time in the atmosphere than HBr, is expected to have a…
View article: Predicting the regional impact of interventions to prevent and contain multidrug-resistant organisms
Predicting the regional impact of interventions to prevent and contain multidrug-resistant organisms Open
Background: Multidrug-resistant organisms (MDROs), such as carbapenem-resistant Enterobacterales (CRE), can spread rapidly in a region. Facilities that care for high-acuity patients with long average lengths of stay (eg, long-term acute-ca…
View article: Increases in methicillin-sensitive Staphylococcus aureus bloodstream infection incidence, 2016–2019
Increases in methicillin-sensitive Staphylococcus aureus bloodstream infection incidence, 2016–2019 Open
Background: Incidence of methicillin-sensitive Staphylococcus aureus (MSSA) bloodstream infections (BSIs) in the United States during 2012–2017 has been reported to have been stable for hospital-onset BSIs and to have increased 3.9% per ye…
View article: CDC COVID-19 healthcare infection prevention and control assistance to health departments, January 2020–December 2021
CDC COVID-19 healthcare infection prevention and control assistance to health departments, January 2020–December 2021 Open
Background: Throughout the COVID-19 pandemic, CDC Division of Healthcare Quality Promotion (DHQP) has provided technical assistance in support of state, tribal, local, and territorial health departments for COVID-19 healthcare outbreak man…
View article: Scalable and robust Firedrake deployment on ARCHER2 and beyond
Scalable and robust Firedrake deployment on ARCHER2 and beyond Open
We summarise the different aspects of Firedrake deployment that we have improved for our HPC users and additional benefits for ARCHER2 users. A Spack package has been created for Firedrake many of its dependencies as well as determining a …
View article: Bringing Trimmed Serendipity Methods to Computational Practice in Firedrake
Bringing Trimmed Serendipity Methods to Computational Practice in Firedrake Open
We present an implementation of the trimmed serendipity finite element family, using the open-source finite element package Firedrake. The new elements can be used seamlessly within the software suite for problems requiring H 1 , H (curl),…
View article: Scalable I/O and Checkpointing for Firedrake
Scalable I/O and Checkpointing for Firedrake Open
Firedrake [1] is a system for solving partial differential equations using finite element methods. In this work we enhance the I/O checkpointing capabilities of Firedrake introducing a new interface. The new interface allows for saving and…
View article: Escaping the abstraction: a foreign function interface for the Unified Form Language [UFL]
Escaping the abstraction: a foreign function interface for the Unified Form Language [UFL] Open
High level domain specific languages for the finite element method underpin high productivity programming environments for simulations based on partial differential equations (PDE) while employing automatic code generation to achieve high …
View article: Escaping the abstraction: a foreign function interface for the Unified\n Form Language [UFL]
Escaping the abstraction: a foreign function interface for the Unified\n Form Language [UFL] Open
High level domain specific languages for the finite element method underpin\nhigh productivity programming environments for simulations based on partial\ndifferential equations (PDE) while employing automatic code generation to\nachieve hi…
View article: ExCALIBUR Research Software Engineer Knowledge Integration Landscape Review
ExCALIBUR Research Software Engineer Knowledge Integration Landscape Review Open
The Research Software Engineer Knowledge Integration Landscape Review was written by the ExCALIBUR Programme Community. It documents the concept of the Research Software Engineer (RSE) and their role in many of todays computational science…
View article: Code Generation for Productive, Portable, and Scalable Finite Element Simulation in Firedrake
Code Generation for Productive, Portable, and Scalable Finite Element Simulation in Firedrake Open
Creating scalable, high performance PDE-based simulations requires an appropriate combination of models,\ndiscretizations, and solvers. The required combination changes with the application and with the available hardware, yet software\nde…
View article: Bringing Trimmed Serendipity Methods to Computational Practice in Firedrake
Bringing Trimmed Serendipity Methods to Computational Practice in Firedrake Open
We present an implementation of the trimmed serendipity finite element family, using the open source finite element package Firedrake. The new elements can be used seamlessly within the software suite for problems requiring $H^1$, \hcurl, …
View article: Code generation for productive portable scalable finite element simulation in Firedrake
Code generation for productive portable scalable finite element simulation in Firedrake Open
Creating scalable, high performance PDE-based simulations requires a suitable combination of discretizations, differential operators, preconditioners and solvers. The required combination changes with the application and with the available…