Martin Alnæs
External collaborator
Publications
Simula-affiliated publications listed
2018
Journal Articles
S. W. Funke, M. Nordaas, Ø. Evju, M. S. Alnæs and K. Mardal
Variational data assimilation for transient blood flow simulations
International Journal for Numerical Methods in Biomedical Engineering
2017
Posters
M. S. Alnæs, J. Blechta, J. S. Hale, A. Logg, C. Richardson, J. Ring, M. E. Rognes and G. N. Wells
FEniCS: Sustainable Software Development Practices
Talks, invited
M. S. Alnæs
The Unified Form Language and Key Points on its Translation
SIAM CSE, Atlanta, USA
Talks, contributed
M. S. Alnæs, V. T. Fauske and B. Ragan-Kelley
3D visualization in Jupyter Notebooks
FEniCS’17, Luxembourg
V. T. Fauske, M. S. Alnæs and B. Ragan-Kelley
Interactive 3D Visualization in Jupyter Notebooks
EuroSciPy 2017, Erlangen, Germany
V. T. Fauske, B. Ragan-Kelley and M. S. Alnæs
Jupyter Notebooks in Source Control: nbdime
PyData London, UK
V. T. Fauske, B. Ragan-Kelley and M. S. Alnæs
Notebooks in Version Control - diffing and merging with nbdime
Computational Mathematics with Jupyter workshop, Edinburgh, Scotland
2016
Journal Articles
G. Balaban, M. S. Alnæs, J. Sundnes and M. E. Rognes
Adjoint Multi-Start Based Estimation of Cardiac Hyperelastic Material Parameters using Shear Data
Biomechanics and Modeling in Mechanobiology
Talks, invited
K. Mardal, S. W. Funke, M. Nordaas, Ø. Evju and M. S. Alnæs
Variational data assimilation for blood flow simulations
MS at SIAM UQ, Zurich
V. T. Fauske, M. S. Alnæs and B. Ragan-Kelley
nbdime: diffing and merging notebooks
JupyterDay Orsay
Talks, contributed
B. Ragan-Kelley, V. T. Fauske and M. S. Alnæs
Diffing and Merging Jupyter Notebooks with nbdime
SciPy 2016
V. T. Fauske, M. S. Alnæs and B. Ragan-Kelley
nbdime: Notebook Diffing and Merging
EuroSciPy 2016, Erlangen, Germany
2015
Journal Articles
M. S. Alnæs, K. Mardal, S. J. Bakke and A. Sorteberg
Computational fluid dynamics evaluation of flow reversal treatment of giant basilar tip aneurysm
Interventional Neuroradiology
K. Støverud, M. S. Alnæs, H. P. Langtangen, V. Haughton and K. Mardal
Poro-elastic modeling of Syringomyelia – a systematic study of the effects of pia mater, central canal, median fissure, white and gray matter on pressure wave propagation and fluid movement within the cervical spinal cord
Computer Methods in Biomechanics and Biomedical Engineering
M. S. Alnæs, J. Blechta, J. E. Hake, A. Johansson, B. Kehlet, A. Logg, C. Richardson, J. Ring, M. E. Rognes and G. N. Wells
The FEniCS Project Version 1.5
Archive of Numerical Software
Talks, invited
M. E. Rognes, B. Kehlet, A. Logg and M. S. Alnæs
Towards a Unified Framework for Automated a Posteriori Error Estimation and Adaptivity in Space-Time
SIAM CSE, Salt Lake City, USA
Talks, contributed
M. E. Rognes, G. Balaban, J. Sundnes and M. S. Alnæs
Identifying the Parameters of the Heart: Variational Data Assimilation in Cardiac Mechanics Using Dolfin-Adjoint
FEniCS '15, Imperial College London, UK
2014
Journal Articles
M. S. Alnæs, A. Logg, K. B. Ølgaard, M. E. Rognes and G. N. Wells
Unified Form Language: a Domain-Specific Language for Weak Formulations of Partial Differential Equations
ACM Transactions on Mathematical Software
Proceedings, non-refereed
G. Balaban, J. Sundnes, M. S. Alnæs and M. E. Rognes
Least Squares Fitting of a Cardiac Hyperelasticity Model Using an Automatically Derived Adjoint Equation
Proceedings of NSCM-27: the 27th Nordic Seminar on Computational Mechanics
Talks, invited
M. S. Alnæs
The Unified Form Language -- Features, implementation and future
PRISM Workshop, Imperial College London
Talks, contributed
M. S. Alnæs
High level abstractions for finite element methods -- The Unified Form Language and the FEniCS project
CBC/Uppsala workshop, Simula Research Laboratory
2013
Talks, contributed
M. S. Alnæs
Computational Investigation of Parent Artery Flow Reversal for Basilar Top Aneurysm
5th Asia Pacific Congress on Computational Mechanics & 4th International Symposium on Computational Mechanics
M. S. Alnæs
Data Assimilation With Navier-Stokes Splitting Schemes and Dolfin-Adjoint
CBC and CCI Workshop on Advancing Numerical Technologies in the Cardiac Domain, May 15
M. S. Alnæs
Status of Effective Translation of Complicated Forms in FEniCS
CBC seminar series
M. S. Alnæs
Status of Effective Translation of Complicated Forms in FEniCS - the UFLACS Project
Jesus College, Cambrigde
M. S. Alnæs
Towards Navier-Stokes Data Assimilation for Hemodynamics Using Automated Adjoint Methods
V International Symposium on Modelling of Physiological Flows (MPF2013)
2012
Book Chapters
I. Wilbers, K. Mardal and M. S. Alnæs
Instant: Just-in-Time Compilation of C/C++ in Python
Automated Solution of Differential Equations by the Finite Element Method
M. S. Alnæs and K. Mardal
SyFi and SFC: Symbolic Finite Elements and Form Compilation
Automated Solution of Differential Equations by the Finite Element Method
M. S. Alnæs, A. Logg and K. Mardal
UFC: a Finite Element Code Generation Interface
Automated Solution of Differential Equations by the Finite Element Method
M. S. Alnæs
UFL: a Finite Element Form Language
Automated Solution of Differential Equations by the Finite Element Method
Talks, invited
M. S. Alnæs
A Domain Specific Language and Symbolic Library for FEM Formulations of PDEs - the Unified Form Language
FEniCS@Imperial Day, Imperial College London
Talks, contributed
M. S. Alnæs
Automation of PDE Constrained Optimization - Algorithmic Differentiation As Abstract Building Blocks in High Level Algorithms
ECCOMAS 2012, Wien
M. S. Alnæs
Efficient Compilation of Complex Tensor Algebra Expressions
FEniCS Workshop 2012, Simula Research Laboratory
K. Mardal, B. F. Nielsen and M. S. Alnæs
Efficient Preconditioning of Optimality Systems
EMG 2012
M. S. Alnæs
News in C++11
CBC Seminar series
M. S. Alnæs
Numerical Comparison of Preconditioned Oneshot and Steepest Descent on Linear Elliptic Optimal Control Problems
OCIP 2012
2011
Talks, invited
K. Mardal, K. Valen-Sendstad, M. S. Alnæs, M. Mortensen, H. P. Langtangen and B. A. P. Reif
The Finite Element Library FEniCS and Simulation of Blood Flow in Cerebral Aneurysms
Talk at CSB Seminar, University of Stuttgart
Talks, contributed
M. S. Alnæs
The Unified Form Language - a Domain Specific Language for Finite Element Methods
European Numerical Mathematics and Advanced Applications (ENUMATH)
2010
Journal Articles
M. S. Alnæs and K. Mardal
On the Efficiency of Symbolic Computations Combined With Code Generation for Finite Element Methods
ACM Transactions on Mathematical Software
2009
Journal Articles
M. S. Alnæs, A. Logg, K. Mardal, O. Skavhaug and H. P. Langtangen
Unified Framework for Finite Element Assembly
International Journal of Computational Science and Engineering
PhD Thesis
M. S. Alnæs
A Compiler Framework for Automatic Linearization and Efficient Discretization of Nonlinear Partial Differential Equations
Talks, contributed
M. S. Alnæs
The Unified Form Language
Presentation at the FEniCS'09 Workshop
M. S. Alnæs
The Unified Form Language
Internal presentation at CBC
Manuals
M. S. Alnæs and A. Logg
UFL Specification and User Manual
2008
Talks, contributed
M. S. Alnæs and K. Mardal
SFC - the SyFi Form Compiler
Talk at the FEniCS 08 Workshop, March 5-7,Baton Rouge, Louisiana
K. Mardal, B. F. Nielsen and M. S. Alnæs
Two Steps Towards Automating Efficient Solution of Inverse Problems
Invited Talk at the FEniCS 08 Workshop, March 5-7,Baton Rouge, Louisiana
2007
Journal Articles
M. S. Alnæs, J. G. Isaksen, K. Mardal, B. Romner, M. K. Morgan and T. Ingebrigtsen
Computation of Hemodynamics in the Circle of Willis
Stroke
Proceedings, refereed
M. S. Alnæs, K. Mardal and J. Sundnes
Application of Symbolic Finite Element Tools to Nonlinear Hyperelasticity
Fourth national conference on Computational Mechanics (MekIT'07)
Book Chapters
A. Logg, K. Mardal, M. S. Alnæs, H. P. Langtangen and O. Skavhaug
A Hybrid Approach to Efficient Finite Element Code Development
Petascale Computing - Algorithms and Applications
Talks, contributed
J. Sundnes, M. S. Alnæs and K. Mardal
A Finite Element Model of Cardiac Electrophysiology and Mechanics
VII International conference on computational plasticity
M. S. Alnæs, K. Mardal and J. Sundnes
Application of Symbolic Finite Element Tools to Nonlinear Hyperelasticity
Talk at MekIT'07: Fourth National Conference on Computational Mechanics
M. S. Alnæs
Computing the Mechanics of the Heart
Talk at CBC, Seminar on Electrophysiology Modeling
Manuals
M. S. Alnæs, A. Logg, K. Mardal, O. Skavhaug and H. P. Langtangen
UFC Specification and User Manual 1.0
2006
Talks, contributed
M. S. Alnæs, A. M. Bruaset, X. Cai, H. P. Langtangen, K. Mardal, H. Moe, O. Skavhaug and Å. Ødegård
Python in High Performance Computing
Tutorial presented at the Para06 Workshop
Manuals
M. S. Alnæs and K. Mardal
SyFi User Manual
2005
Talks, contributed
M. S. Alnæs
Scientific Computing in Python
Tutorial, ASIM 2005
A. M. Bruaset, M. S. Alnæs, H. P. Langtangen, K. Mardal, H. Moe, O. Skavhaug and Å. Ødegård
Scientific Computing in Python
Tutorial ASIM 2005