## How to cite

If you use Dedalus in your work, we ask that you cite the Dedalus methods paper:

K J Burns, G M Vasil, J S Oishi, D Lecoanet, B P Brown, "Dedalus: A Flexible Framework for Numerical Simulations with Spectral Methods," Physical Review Research, vol. 2, no. 2, p. 838, Apr. 2020. [doi] [arxiv] [bibtex] [examples]

## Papers about Dedalus

K J Burns, G M Vasil, J S Oishi, D Lecoanet, B P Brown, "Dedalus: A flexible framework for numerical simulations with spectral methods," Physical Review Research, vol. 2, no. 2, p. 838, Apr 2020. [doi]

G M Vasil, D Lecoanet, K J Burns, J S Oishi, B P Brown, "Tensor calculus in spherical coordinates using Jacobi polynomials. Part-I: Mathematical analysis and derivations," Journal of Computational Physics: X, vol. 3, p. 100013, Jun 2019. [doi]

D Lecoanet, G M Vasil, K J Burns, B P Brown, J S Oishi, "Tensor calculus in spherical coordinates using Jacobi polynomials. Part-II: Implementation and examples," Journal of Computational Physics: X, vol. 3, p. 100012, Jun 2019. [doi]

J S Oishi, B P Brown, K J Burns, D Lecoanet, G M Vasil, "Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software from Seven Years of the Dedalus Project," arXiv.org, p. arXiv:1801.08200, Jan 2018. [arxiv]

G M Vasil, K J Burns, D Lecoanet, S Olver, B P Brown, J S Oishi, "Tensor calculus in polar coordinates using Jacobi polynomials," Journal of Computational Physics, vol. 325, pp. 53-73, Nov 2016. [doi]

## Papers & preprints using Dedalus

If you have work using Dedalus that you would like to have listed here, please let us know!

N Bhamidipati, A W Woods, "Shear generation in a confined, composite layer of cross-bedded porous rock," Journal of Fluid Mechanics, vol. 899, p. R3, Sep 2020. [doi]

N Lahaye, V Zeitlin, T Dubos, "Coherent dipoles in a mixed layer with variable buoyancy: Theory compared to observations," Ocean Modelling, vol. 153, p. 101673, Sep 2020. [doi]

S Gururaj, A Guha, "Energy transfer in resonant and near-resonant internal wave triads for weakly non-uniform stratifications. Part 1. Unbounded domain," Journal of Fluid Mechanics, vol. 899, p. A6, Sep 2020. [doi]

S D Bachman, "A Geometric Perspective on the Modulation of Potential Energy Release by a Lateral Potential Vorticity Gradient," Fluids, vol. 5, no. 3, p. 142, Sep 2020. [doi]

B P Brown, J S Oishi, G M Vasil, D Lecoanet, K J Burns, "Single-hemisphere dynamos in M-dwarf stars," arXiv.org, p. arXiv:2008.02362, Aug 2020. [arxiv]

L K Currie, S M Tobias, "Generation of shear flows and vortices in rotating anelastic convection," Physical Review Fluids, vol. 5, no. 7, p. 446, Jul 2020. [doi]

C B Rocha, N C Constantinou, S G Llewellyn Smith, W R Young, "The Nusselt numbers of horizontal convection," Journal of Fluid Mechanics, vol. 894, p. 6, Jul 2020. [doi]

J R Fuentes, A Cumming, "Penetration of a cooling convective layer into a stably-stratified composition gradient: entrainment at low Prandtl number," arXiv.org, Jul 2020. [arxiv]

A T Clarke, C J Davies, D Ruprecht, S M Tobias, "Parallel-in-time integration of kinematic dynamos," Journal of Computational Physics: X, vol. 7, p. 100057, Jun 2020. [doi]

J O Wenegrat, L N Thomas, "Centrifugal and Symmetric Instability during Ekman Adjustment of the Bottom Boundary Layer," Journal of Physical Oceanography, vol. 50, no. 6, pp. 1793-1812, Jun 2020. [doi]

P Kooloth, D Sondak, L M Smith, "Coherent Solutions and Transition to Turbulence in Two-Dimensional Rayleigh-Bénard Convection," arXiv.org, Jun 2020. [arxiv]

E W Hester, L A Couston, B Favier, K J Burns, G M Vasil, "Improved phase-field models of melting and dissolution in multi-component flows," arXiv.org, p. arXiv:2006.16004, Jun 2020. [arxiv]

D N Hosking, A A Schekochihin, S A Balbus, "Elasticity of tangled magnetic fields," arXiv.org, p. arXiv:2006.15141, Jun 2020. [arxiv]

R Supekar, V Heinonen, K J Burns, J Dunkel, "Linearly forced fluid flow on a rotating sphere," Journal of Fluid Mechanics, vol. 892, p. 1, Jun 2020. [doi]

N Bhamidipati, A N Souza, G R Flierl, "Turbulent mixing of a passive scalar in the ocean mixed layer," Ocean Modelling, vol. 149, p. 101615, May 2020. [doi]

Y Zhang, S I Krasheninnikov, R Masline, R D Smirnov, "Anomalous edge plasma transport, neutrals, and divertor plasma detachment," arXiv.org, p. arXiv:2005.13493, May 2020. [arxiv]

J B Parker, J B Marston, S M Tobias, Z Zhu, "Topological Gaseous Plasmon Polariton in Realistic Plasma," Physical Review Letters, vol. 124, no. 19, p. 195001, May 2020. [doi]

Y Su, D Lecoanet, D Lai, "Physics of tidal dissipation in early-type stars and white dwarfs: hydrodynamical simulations of internal gravity wave breaking in stellar envelopes," Monthly Notices of the Royal Astronomical Society, vol. 495, no. 1, pp. 1239-1251, May 2020. [doi]

C M Jiang, S Esmaeilzadeh, K Azizzadenesheli, K Kashinath, M Mustafa, H A Tchelepi, P Marcus, Prabhat, A Anandkumar, "MeshfreeFlowNet: A Physics-Constrained Deep Continuous Space-Time Super-Resolution Framework," arXiv.org, p. arXiv:2005.01463, May 2020. [arxiv]

L A Couston, D Lecoanet, B Favier, M Le Bars, "Shape and size of large-scale vortices: A generic fluid pattern in geophysical fluid dynamics," Physical Review Research, vol. 2, no. 2, p. 023143, May 2020. [doi]

C D Marcotte, V N Biktashev, "Predicting critical ignition in slow-fast excitable models," Physical Review E, vol. 101, no. 4, p. 311, Apr 2020. [doi]

L A Couston, E Hester, B Favier, J R Taylor, P R Holland, A Jenkins, "Ice melting in a turbulent stratified shear flow," arXiv.org, Apr 2020. [arxiv]

S Kar, A Guha, "An inverse technique for reconstructing ocean\textquoterights density stratification from surface data," Ocean Modelling, vol. 147, p. 101561, Mar 2020. [doi]

Y Zhou, H Zhu, I Y Dodin, "Solitary zonal structures in subcritical drift waves: a minimum model," Plasma Physics and Controlled Fusion, vol. 62, no. 4, p. 045021, Mar 2020. [doi]

E H Anders, G M Vasil, B P Brown, L Korre, "Convective dynamics with mixed temperature boundary conditions: why thermal relaxation matters and how to accelerate it," arXiv.org, p. arXiv:2003.00026, Feb 2020. [arxiv]

A Farhat, N E Glatt-Holtz, V R Martinez, S A McQuarrie, J P Whitehead, "Data Assimilation in Large Prandtl Rayleigh--Bénard Convection from Thermal Measurements," SIAM Journal on Applied Dynamical Systems, vol. 19, no. 1, pp. 510-540, Feb 2020. [doi]

M Marciani, P Delplace, "Chiral Maxwell waves in continuous media from Berry monopoles," Physical Review A, vol. 101, no. 2, p. 1804, Feb 2020. [doi]

H Zhu, Y Zhou, I Y Dodin, "Theory of the Tertiary Instability and the Dimits Shift from Reduced Drift-Wave Models," Physical Review Letters, vol. 124, no. 5, p. 055002, Feb 2020. [doi]

J Olsthoorn, C E Bluteau, G A Lawrence, "Under-ice salinity transport in low-salinity waterbodies," Limnology and Oceanography, vol. 65, no. 2, pp. 247-259, Feb 2020. [doi]

C Tauber, P Delplace, A Venaille, "Anomalous bulk-edge correspondence in continuous media," Physical Review Research, vol. 2, no. 1, p. 123, Feb 2020. [doi]

L K Currie, A J Barker, Y Lithwick, M K Browning, "Convection with misaligned gravity and rotation: simulations and rotating mixing length theory," Monthly Notices of the Royal Astronomical Society, vol. 493, no. 4, pp. 5233-5256, Feb 2020. [doi]

X Ruan, J Callies, "Mixing-Driven Mean Flows and Submesoscale Eddies over Mid-Ocean Ridge Flanks and Fracture Zone Canyons," Journal of Physical Oceanography, vol. 50, no. 1, pp. 175-195, Jan 2020. [doi]

E Carlson, J Hudson, A Larios, "Parameter Recovery for the 2 Dimensional Navier--Stokes Equations via Continuous Data Assimilation," SIAM Journal on Scientific Computing, vol. 42, no. 1, pp. A250-A270, Jan 2020. [doi]

J S Oishi, G M Vasil, M Baxter, A Swan, K J Burns, D Lecoanet, B P Brown, "The magnetorotational instability prefers three dimensions," Proc R Soc A, vol. 476, no. 2233, p. 20190622, Jan 2020. [doi]

C B Rocha, T Bossy, S G Llewellyn Smith, W R Young, "Improved bounds on horizontal convection," Journal of Fluid Mechanics, vol. 883, p. 5957, Jan 2020. [doi]

B McKim, N Jeevanjee, D Lecoanet, "Buoyancy-driven entrainment in dry thermals," Quarterly Journal of the Royal Meteorological Society, vol. 146, no. 726, pp. 415-425, Jan 2020. [doi]

A Clarke, C Davies, D Ruprecht, S Tobias, J S Oishi, "Performance of parallel-in-time integration for Rayleigh Bénard Convection," arXiv.org, p. arXiv:2001.01609, Jan 2020. [arxiv]

P Pearce, B Song, D J Skinner, R Mok, R Hartmann, P K Singh, H Jeckel, J S Oishi, K Drescher, J Dunkel, "Flow-Induced Symmetry Breaking in Growing Bacterial Biofilms," Physical Review Letters, vol. 123, no. 25, p. 258101, Dec 2019. [doi]

L Siegelman, P Klein, P Rivière, A F Thompson, H S Torres, M Flexas, D Menemenlis, "Enhanced upward heat transport at deep submesoscale ocean fronts," Nature Geoscience, vol. 13, no. 1, pp. 50-55, Dec 2019. [doi]

D Lecoanet, N Jeevanjee, "Entrainment in Resolved, Dry Thermals," Journal of the Atmospheric Sciences, vol. 76, no. 12, pp. 3785-3801, Nov 2019. [doi]

D Lecoanet, M Cantiello, E Quataert, L A Couston, K J Burns, B J S Pope, A S Jermyn, B Favier, M Le Bars, "Low-frequency Variability in Massive Stars: Core Generation or Surface Phenomenon?," The Astrophysical Journal Letters, vol. 886, no. 1, p. L15, Nov 2019. [doi]

E H Anders, D Lecoanet, B P Brown, "Entropy Rain: Dilution and Compression of Thermals in Stratified Domains," The Astrophysical Journal, vol. 884, no. 1, p. 65, Oct 2019. [doi]

R M Holmes, C de Lavergne, T J McDougall, "Tracer Transport within Abyssal Mixing Layers," Journal of Physical Oceanography, vol. 49, no. 1, pp. 2669-2695, Oct 2019. [doi]

J Olsthoorn, E W Tedford, G A Lawrence, "Diffused-interface Rayleigh-Taylor instability with a nonlinear equation of state," Physical Review Fluids, vol. 4, no. 9, p. 094501, Sep 2019. [doi]

J B Parker, J W Burby, J B Marston, S M Tobias, "Nontrivial topology of the Alfvén continuum and topological character of reversed-shear Alfvén eigenmodes," arXiv.org, p. arXiv:1909.07910, Sep 2019. [arxiv]

J B Parker, N C Constantinou, "Magnetic eddy viscosity of mean shear flows in two-dimensional magnetohydrodynamics," Physical Review Fluids, vol. 4, no. 8, p. 083701, Aug 2019. [doi]

S Davidovits, N J Fisch, "Viscous dissipation in two-dimensional compression of turbulence," Physics of Plasmas, vol. 26, no. 8, p. 082702, Aug 2019. [doi]

M Perrot, P Delplace, A Venaille, "Topological transition in stratified fluids," Nature Physics, vol. 15, no. 8, pp. 781-784, Jun 2019. [doi]

C Tauber, P Delplace, A Venaille, "A bulk-interface correspondence for equatorial waves," Journal of Fluid Mechanics, vol. 868, p. 123, Jun 2019. [doi]

V Heinonen, K J Burns, J Dunkel, "Quantum hydrodynamics for supersolid crystals and quasicrystals," Physical Review A, vol. 99, no. 6, p. 063621, Jun 2019. [doi]

E Quataert, D Lecoanet, E R Coughlin, "Black hole accretion discs and luminous transients in failed supernovae from non-rotating supergiants," Monthly Notices of the Royal Astronomical Society: Letters, vol. 485, no. 1, pp. L83-L88, Mar 2019. [doi]

E W Hester, G M Vasil, K J Burns, "Improving convergence of volume penalized fluid-solid interactions," arXiv.org, p. arXiv:1903.11914, Mar 2019. [arxiv]

K J Burns, D Lecoanet, G M Vasil, J S Oishi, B P Brown, "The "Sphered Cube": A New Method for the Solution of Partial Differential Equations in Cubical Geometry," arXiv.org, p. arXiv:1903.12642, Mar 2019. [arxiv]

L K Currie, S M Tobias, "Convection-driven kinematic dynamos with a self-consistent shear flow," Geophysical & Astrophysical Fluid Dynamics, vol. 113, no. 1-2, pp. 131-148, Mar 2019. [doi]

G Michel, G P Chini, "Multiple scales analysis of slow--fast quasi-linear systems," Proc R Soc A, vol. 475, no. 2223, p. 20180630, Mar 2019. [doi]

M Mussel, M F Schneider, "It sounds like an action potential: unification of electrical, chemical and mechanical aspects of acoustic pulses in lipids," Journal of The Royal Society Interface, vol. 16, no. 151, p. 20180743, Feb 2019. [doi]

M Mussel, M F Schneider, "Similarities between action potentials and acoustic pulses in a van der Waals fluid," Scientific Reports, vol. 9, no. 1, p. 73, Feb 2019. [doi]

G Michel, G P Chini, "Strong wave--mean-flow coupling in baroclinic acoustic streaming," Journal of Fluid Mechanics, vol. 858, pp. 536-564, Jan 2019. [doi]

G K Vallis, D J Parker, S M Tobias, "A simple system for moist convection: the~Rainy--Bénard model," Journal of Fluid Mechanics, vol. 862, pp. 162-199, Jan 2019. [doi]

A E Fraser, M J Pueschel, P W Terry, E G Zweibel, "Role of stable modes in driven shear-flow turbulence," Physics of Plasmas, vol. 25, no. 12, p. 122303, Dec 2018. [doi]

L A Couston, D Lecoanet, B Favier, M Le Bars, "The energy flux spectrum of internal waves generated by turbulent convection," Journal of Fluid Mechanics, vol. 854, p. 1103, Nov 2018. [doi]

S M Tobias, J S Oishi, J B Marston, "Generalized quasilinear approximation of the interaction of convection and mean flows in a thermal annulus," Proc R Soc A, vol. 474, no. 2219, p. 20180422, Nov 2018. [doi]

J O Wenegrat, J Callies, L N Thomas, "Submesoscale Baroclinic Instability in the Bottom Boundary Layer," Journal of Physical Oceanography, vol. 48, no. 11, pp. 2571-2592, Nov 2018. [doi]

S Lepot, S Aumaître, B Gallet, "Radiative heating achieves the ultimate regime of thermal convection," Proceedings of the National Academy of Sciences, vol. 115, no. 36, pp. 8937-8941, Sep 2018. [doi]

J Callies, "Restratification of Abyssal Mixing Layers by Submesoscale Baroclinic Eddies," Journal of Physical Oceanography, vol. 48, no. 9, pp. 1995-2010, Sep 2018. [doi]

N Tarshish, N Jeevanjee, D Lecoanet, "Buoyant Motion of a Turbulent Thermal," Journal of the Atmospheric Sciences, vol. 75, no. 9, pp. 3233-3244, Sep 2018. [doi]

G Saranraj, A Guha, "Energy transfer in resonant and near-resonant internal wave triads for weakly non-uniform stratifications. Part I: Unbounded domain," arXiv.org, p. arXiv:1808.05591, Aug 2018. [arxiv]

N Balci, A M Isenberg, M S Jolly, "Turbulence in vertically averaged convection," Physica D: Nonlinear Phenomena, vol. 376-377, pp. 216-227, Aug 2018. [doi]

E H Anders, B P Brown, J S Oishi, "Accelerated evolution of convective simulations," Physical Review Fluids, vol. 3, no. 8, p. 083502, Aug 2018. [doi]

J H Kim, W Moon, A J Wells, J P Wilkinson, T Langton, B Hwang, M A Granskog, D W Rees Jones, "Salinity Control of Thermal Evolution of Late Summer Melt Ponds on Arctic Sea Ice," Geophysical Research Letters, vol. 45, no. 16, pp. 8304-8313, Aug 2018. [doi]

L A Couston, D Lecoanet, B Favier, M Le Bars, "Order Out of Chaos: Slowly Reversing Mean Flows Emerge from Turbulently Generated Internal Waves," Physical Review Letters, vol. 120, no. 24, p. 244505, Jun 2018. [doi]

O Mickelin, J Słomka, K J Burns, D Lecoanet, G M Vasil, L M Faria, J Dunkel, "Anomalous Chained Turbulence in Actively Driven Flows on Spheres," Physical Review Letters, vol. 120, no. 16, p. 164503, Apr 2018. [doi]

B Bordwell, B P Brown, J S Oishi, "Convective Dynamics and Disequilibrium Chemistry in the Atmospheres of Giant Planets and Brown Dwarfs," The Astrophysical Journal, vol. 854, no. 1, p. 8, Feb 2018. [doi]

D Lecoanet, R R Kerswell, "Connection between nonlinear energy optimization and instantons," Physical Review E, vol. 97, no. 1, p. 012212, Jan 2018. [doi]

D Seligman, G Laughlin, "A Vorticity-preserving Hydrodynamical Scheme for Modeling Accretion Disk Flows," The Astrophysical Journal, vol. 848, no. 1, p. 54, Oct 2017. [doi]

L A Couston, D Lecoanet, B Favier, M Le Bars, "Dynamics of mixed convective--stably-stratified fluids," Physical Review Fluids, vol. 2, no. 9, p. 094804, Sep 2017. [doi]

L K Currie, M K Browning, "The Magnitude of Viscous Dissipation in Strongly Stratified Two-dimensional Convection," The Astrophysical Journal Letters, vol. 845, no. 2, p. L17, Aug 2017. [doi]

E H Anders, B P Brown, "Convective heat transport in stratified atmospheres at low and high Mach number," Physical Review Fluids, vol. 2, no. 8, p. 083501, Aug 2017. [doi]

S E Clark, J S Oishi, "The Weakly Nonlinear Magnetorotational Instability in a Global, Cylindrical Taylor--Couette Flow," The Astrophysical Journal, vol. 841, no. 1, p. 2, May 2017. [doi]

S E Clark, J S Oishi, "The Weakly Nonlinear Magnetorotational Instability in a Local Geometry," The Astrophysical Journal, vol. 841, no. 1, p. 1, May 2017. [doi]

J Földes, N Glatt-Holtz, G Richards, J Whitehead, "Hydrodynamic stability in the presence of a stochastic forcing:a case study in convection," arXiv.org, p. arXiv:1704.03840, Apr 2017. [arxiv]

D Lecoanet, G M Vasil, J Fuller, M Cantiello, K J Burns, "Conversion of internal gravity waves into magnetic waves," Monthly Notices of the Royal Astronomical Society, vol. 466, no. 2, pp. 2181-2193, Jan 2017. [doi]

S Davidovits, N J Fisch, "Compressing turbulence and sudden viscous dissipation with compression-dependent ionization state," Physical Review E, vol. 94, no. 5, p. 683, Nov 2016. [doi]

S M Tobias, J B Marston, "Three-dimensional rotating Couette flow via the generalised quasilinear approximation," Journal of Fluid Mechanics, vol. 810, pp. 412-428, Nov 2016. [doi]

D Lecoanet, J Schwab, E Quataert, L Bildsten, F X Timmes, K J Burns, G M Vasil, J S Oishi, B P Brown, "Turbulent Chemical Diffusion in Convectively Bounded Carbon Flames," The Astrophysical Journal, vol. 832, no. 1, p. 71, Nov 2016. [doi]

S Davidovits, N J Fisch, "Sudden Viscous Dissipation of Compressing Turbulence," Physical Review Letters, vol. 116, no. 10, p. 683, Mar 2016. [doi]

D Lecoanet, M McCourt, E Quataert, K J Burns, G M Vasil, J S Oishi, B P Brown, J M Stone, R M O'Leary, "A validated non-linear Kelvin--Helmholtz benchmark for numerical hydrodynamics," Monthly Notices of the Royal Astronomical Society, vol. 455, no. 4, pp. 4274-4288, Dec 2015. [doi]

D Lecoanet, M Le Bars, K J Burns, G M Vasil, B P Brown, E Quataert, J S Oishi, "Numerical simulations of internal wave generation by convection in water," Physical Review E, vol. 91, no. 6, p. 320, Jun 2015. [doi]

G M Vasil, "On the magnetorotational instability and elastic buckling," Proc R Soc A, vol. 471, no. 2177, pp. 20140699-20140699, Apr 2015. [doi]

D Lecoanet, B P Brown, E G Zweibel, K J Burns, J S Oishi, G M Vasil, "Conduction in Low Mach Number Flows. I. Linear and Weakly Nonlinear Regimes," The Astrophysical Journal, vol. 797, no. 2, p. 94, Dec 2014. [doi]