**REFEREED Publications**

- Kalogirou A; Bokhove O; Ham D (2017) Modelling of nonlinear wave-buoy dynamics using constrained variational methods Proceedings of the International Conference on Offshore Mechanics and Arctic Engineering - OMAE. Proceedings of the International Conference on Offshore Mechanics and Arctic Engineering - OMAE, doi:10.1115/OMAE2017-61966
- Kalogirou A; Bokhove O (2016) Mathematical and numerical modelling of wave impact on wave-energy buoys Proceedings of the International Conference on Offshore Mechanics and Arctic Engineering - OMAE. Proceedings of the International Conference on Offshore Mechanics and Arctic Engineering - OMAE, doi:10.1115/OMAE2016-54937
- Presentation at workshop in Vienna 2017 with work-to-date on slide 5: On variational water wave modeling â€”with buoys/symmetric ships, including dates and links.

- 55. Salwa, Bokhove, Kelmanson 2017:
- Variational modelling of wave-structure interactions with an offshore wind-turbine mast. J. Eng. Maths. Firedrake: numerics demo available
- 54. Tom Kent, O.B., Steve Tobias 2017:
- A modified shallow water model for investigating convective-scale data assimilation. Tellus A DOI. GitHub: numerical model available
- 53. Floriane Gidel, O.B., Anna Kalogirou 2017:
- Variational modelling of extreme waves through oblique interaction of solitary waves.
*Nonlinear Processes in Geophys.***24**, 43-60. Firedrake: numerics demo. Zenodo: numerics all simulations. - Variational modelling of extreme waves through oblique interaction of solitary waves.
- 52. Sander van Oers, Leo Maas, O.B. 2017:
- Hamiltonian discontinuous Galerkin Finite Element Method for Internal Gravity Waves
*J. Comp. Phys.***330**, 770-793 - Hamiltonian discontinuous Galerkin Finite Element Method for Internal Gravity Waves
- 51. A. Kalogirou, E.E. Moulopoulou, O.B. 2016:
- Variational finite element method for Waves in a Hele-Shaw Tank.
*Appl. Math. Modelling.*doi: 10.1016/j.apm.2016.02.036 - Variational finite element method for Waves in a Hele-Shaw Tank.
- 50. E. Gagarina, V.R. Ambati, S. Nurijanyan, J.J.W. van der Vegt and O.B. 2016:
- On variational and symplectic time integrators for Hamiltonian systems.

J. Comp. Phys. 306, 370-389. DOI (Ch. 3 of Gagarina's PhD Thesis with test from Ch. 4). - On variational and symplectic time integrators for Hamiltonian systems.
- 49. O.B. and Anna Kalogirou 2016:
- Variational Water Wave Modelling: from Continuum to Experiment.

Lecture Notes on the Theory of Water Waves, Edited by: Bridges, Groves and Nicholls, London Mathematical Society Lecture Notes Series**426**, 226-259 (including simulation of soliton splash w. Benney-Luke system). Firedrake: numerics demo. GitHub: numerics all simulations. - Variational Water Wave Modelling: from Continuum to Experiment.
- 48. A. Thornton, Bram van der Horn, Elena Gagarina, Devaraj van der Meer, Wout Zweers, O.B. 2014:
- Hele-Shaw Beach Creation by Breaking Waves.
*Env. Fluid Dyn.*14, 1123-1145. DOI - Hele-Shaw Beach Creation by Breaking Waves.
- 48a. Onno Bokhove, Bram van der Horn, Devaraj van der Meer, Anthony Thornton, Wout Zweers 2014:
- On wave-driven ``shingle'' beach dynamics in a table-top Hele-Shaw cell. Proc. Int. Conf. Coastal Engineering, Seoul, 2014. 15 pp.
- (Preprint available upon request, including a section on building the Hele-Shaw cell.)
- 47. W. Kristina, O.B. and B. van Groesen 2014:
- Effective coastal boundary conditions for tsunami wave run-up over sloping bathymetry. Nonl. Proc. Geophys. 21, 987-1005.
- 46. E. Gagarina, V.R. Ambati, J van der Vegt and O.B. 2014:
- Variational space-time DGFEM for nonlinear free surface waves.
*J. Comp Phys.*275, 459-483.- Download DOI [Note that version in this link is incorrect: incorrect eprint; mistake Van der Vegt, corrected by Ambati, Bokhove, etc; had asked this version to be removed; version does not have my permission to be online; example of ``Dutch/Twents science''. The swapping of the integral boundaries in (17) is incorrect for moving boundaries and the evaluation in (21) is dubious. Using the original 2011-2012 derivations (draft 2011 one here) that had led to the working codes, this was all corrected in the revision; discussion about it was categorically refused and dismissed Trumpian-style as "an opinion"; I had taken Dr Ambati's doubts, which triggered the corrections in the revision, seriously. I thought I could refute them but they turned out to be correct, signalling mistakes. Dutch funding agency NWO does not care about fixing mistakes: they declared this first-year integral swapping mistake to be very difficult, frontier science in order to avoid declaring it a mistake that needed fixing. Dutch science for you.]
- Variational space-time DGFEM for nonlinear free surface waves.
- 45. D. Tunuguntla, O.B., A. Thornton 2014:
- A mixture theory for size and density segregation in shallow granular free-surface flows.
*J. Fluid Mech.*749. - A mixture theory for size and density segregation in shallow granular free-surface flows.
- 44. S. Nurijanyan, O.B. and L.R.M. Maas 2013:
- Inertial waves in a cuboid. Note on series solutions. Phys. Fluids
**25**126601 eprint & Download DOI - Inertial waves in a cuboid. Note on series solutions. Phys. Fluids
- 43. E. Gagarina, J.J.W. van der Vegt and O.B. 2013:
- Horizontal Circulation and Jumps in Hamiltonian Water Wave Model.

*Nonlinear Processes in Geophysics***20**, 483-500. Paper & eprint - Horizontal Circulation and Jumps in Hamiltonian Water Wave Model.
- 42. S. Nurijanyan, J.J.W. van der Vegt, O.B. 2013:
- Hamiltonian DGFEM for rotating linear incompressible Euler equations: inertial waves -download eprint. J. Comp. Phys. 241, 502-525. Download paper/DOI
- 41. Thornton, Weinhart, Luding, O.B. 2012:
Frictional dependence of shallow granular flows from particle simulations.
- Eur. Phys. J.
**35**, 127. eprints. Level 2/3. - Eur. Phys. J.
- 40. Thornton, Weinhart, Luding, O.B. 2012:
Modelling of particle size segregation: calibration using the discrete particle method.
- Int. J. Mod. Phys. C.
**23**, 1240014. eprints Level 2. - Int. J. Mod. Phys. C.
- 39. Weinhart, Thornton, Luding, O.B. 2012:
- From granular particles to continuum fields near a bounday. Special Issue. Granular Matter
**14**, 289-294. eprints.

Level 4 paper but was scaled down to level 3? Mind you, all these 4 granular papers have high citations even though only 1 is level 4 imo. - From granular particles to continuum fields near a bounday. Special Issue. Granular Matter
- 38. Weinhart, Thornton, Luding, O.B. 2012:
- Closure relations for shallow granular flows from particle simulations. Granular Matter
**14**, 531-552. eprints.Level 3. - Closure relations for shallow granular flows from particle simulations. Granular Matter
- 37. O.B., Elena Gagarina, Wout Zweers, Anthony Thornton 2011: Bore Soliton Splash -van spektakel tot oceaangolf?
- Ned. Tijdschrift voor Natuurkunde. Popular science version in Dutch.
**77/12**, 446-450 - Ned. Tijdschrift voor Natuurkunde. Popular science version in Dutch.
- 36. Sollie, Van der Vegt and Bokhove 2011:
- Space-time discontinuous Galerkin Finite Element Method for two-fluid flows. J. Comp. Physics 230, 789-817.
- 35. C. Cotter and O. Bokhove 2010:
- Water wave model with accurate dispersion and vertical vorticity. Peregrine Commemorative Issue
*J. Eng. Maths.***67**, 33-54. Download eprint & link - Water wave model with accurate dispersion and vertical vorticity. Peregrine Commemorative Issue
- 34. O. Bokhove and Marcel Oliver 2009:
- Hamiltonian N layer model for atmospheric dynamics. (memo 2008)
*Geophys. Astrophys. Fluid Dyn.***103**(6), 423-442. Download DOI - Hamiltonian N layer model for atmospheric dynamics. (memo 2008)
- 33. Onno Bokhove and Vijaya R. Ambati 2009:
Hybrid Rossby-shelf modes in a laboratory ocean.
*J. Phys. Ocean.***39**(10), 2523-2542.- Part of special collection in honour of Joe Pedlosky's 70th birthday in 2008.
- Hybrid Rossby-shelf modes simulation with discontinuous Galerkin FEM: potential vorticity "omega" and streamfunction Psi
- Laboratory visualizations: Hybrid Rossby-shelf mode travelling through a cylindrical laboratory ocean
- 32. Sander Rhebergen, Onno Bokhove, and Jaap van der Vegt, 2009:
- Discontinuous Galerkin finite element methods for shallow two-phase flows.
*CMAME***198**, 819-830. - Discontinuous Galerkin finite element methods for shallow two-phase flows.
- 31. Ben Akers and Onno Bokhove, 2008:
Hydraulic flow through a contraction: multiple steady states.
eprints.
*Phys. Fluids.***20**, 056601.- Movie (Akers & B. '05): multiple steady states in horizontal channel; pink water; bird's eye view.
- Movie (Akers & B. '07): reservoir state.
- 30. Y. Xu, J.J.W. van der Vegt, and O. Bokhove, 2008:
- Discontinuous Hamiltonian Finite Element Method for a Bilinear Poisson Bracket.
*J. Sci. Comput.***35**, 242-265.

doi:10.1007/s10915-008-9191-y. Link to journal.

Based on a Finite Volume exercise vi of Bokhove in the course (2005) numerical techniques for PDE's.

**Simple exercise led to thesis Shavarsh Nurijanyan, papers in 2013 & 2017 and Will Booker's work. Example of Leeds' research-led teaching.** - Discontinuous Hamiltonian Finite Element Method for a Bilinear Poisson Bracket.
- 29. P. Tassi, S. Rhebergen, C. Vionnet, and O. Bokhove, 2008:
- A discontinuous Galerkin finite element model for bed evolution under shallow flows.
*Comp. Methods Appl. Mech. Eng.***197**, 2930-2947. pdf. - A discontinuous Galerkin finite element model for bed evolution under shallow flows.
- 28. Sander Rhebergen, Onno Bokhove, and Jaap van der Vegt, 2008:
- Discontinuous Galerkin finite element methods for hyperbolic nonconservative partial differential equations.
*J. Comp. Phys.***227**, 1887-1922.

**Level 4 paper with high citations & leading to JCP 2014, 2016 papers, Lecture notes 2016 with Anna Kalogirou,**

papers with Floriane Gidel, i.e. my work on DGFEM variational time integrators. - Discontinuous Galerkin finite element methods for hyperbolic nonconservative partial differential equations.
- 27. V.R. Ambati and O. Bokhove, 2007:
- Space-time discontinuous Galerkin discretization of rotating shallow water equations.
*J. Comp. Phys.***225**, 1233-1261. eprints. - Space-time discontinuous Galerkin discretization of rotating shallow water equations.
- 26. Van der Vegt, J.J.W., Iszak, F, and Bokhove, O. 2007:
- Error analysis of a continuous-discontinuous Galerkin finite element model for generalized 2D vorticity dynamics.
*Siam J. Num. Anal.***45**, 1349 eprints. - Error analysis of a continuous-discontinuous Galerkin finite element model for generalized 2D vorticity dynamics.
- 25. Bokhove, O. and P. Lynch 2007:
Air parcel and air particles: Hamiltonian dynamics.
*Nieuw Archief voor Wiskunde***5**, 100-106. eprints.- (Accessible article for wider scientific audience. Two reviewers including one focussing especially on mathematical content.)
- 24. L. Pesch, A. Bell, W.E.H. Sollie, V.R. Ambati, O. Bokhove and J.J.W. van der
Vegt, 2007:
- hpGEM- A software framework for Discontinuous Galerkin finite element methods,
*ACM Transactions on Software***33 (4)**. link. - hpGEM- A software framework for Discontinuous Galerkin finite element methods,
- 23. A.W. Vreman, M. Al-Tarazi, J.A.M. Kuipers, M. van Sint Annaland, and O. Bokhove 2007:
- Supercritical shallow granular flow through a contraction: experiment, theory and simulation.
*J. Fluid Mech.***578**, 233-269 See: Text Vreman et al. - Supercritical shallow granular flow through a contraction: experiment, theory and simulation.
- 22. P. Tassi, O. Bokhove, and C. Vionnet, 2007:
- Space discontinuous Galerkin method for shallow water flows -kinetic and HLLC flux, and potential vorticity-generation.
*Advances in water resources***30**, 998-1015. - Space discontinuous Galerkin method for shallow water flows -kinetic and HLLC flux, and potential vorticity-generation.
- 21. V.R. Ambati and O. Bokhove, 2007:
- Space-time finite element shallow water flows.
*J. Comp. Appl. Math.***204 (2)**, 452-462. - Space-time finite element shallow water flows.
- 20. E. Bernsen, O. Bokhove, and D. van der Sar, 2006:
- Numerical prediction of rose growth.
*Acta Horticulturae.***718**, 89-96. Full text with appendices. - Numerical prediction of rose growth.
- 19. Bokhove, O. and Oliver, M. 2006:
*Proc. Roy. Soc. A.***462**, 2575-2592.

Parcel Eulerian-Lagrangian fluid dynamics for rotating geophysical flows.**Explains parcel view of Hamiltonian dynamics of GFD flows with easiest proof of Jacobi Identity for nontrivial noncanonical Hamiltonian dynamics. Undervalued, yet level 4 paper.** - 18. Bernsen, E., Bokhove, O.and Van der Vegt, J.J.W. 2006:
- A (Dis)Continuous Finite Element Model for Generalized 2D Vorticity Dynamics.
*J. Comp. Phys.***212**, 719-747. technical appendices. Memo. 1787 Dept. of Applied Math., Univ. of Twente. ISSN 0169-2690. Based on 2003 MSc thesis of Erik Bernsen & Novel simulations separatrix dynamics relevant to atmosphere - A (Dis)Continuous Finite Element Model for Generalized 2D Vorticity Dynamics.
- 17. Woods, A.W., Bokhove, O., Boer de, A., Hill, B.E. 2006:
- Compressible magma flow in a two-dimensional elastic-walled conduit.
*Earth Planet. Sci. Lett.***246**, 241-250. - Compressible magma flow in a two-dimensional elastic-walled conduit.
- 16. O. Bokhove, 2005:
Hamiltonian restriction of Vlasov equations into two-layer isopycnic and isentropic equations.
*Applied Math. Lett.***18**, 1418-1425. - 15. Bokhove, O., Woods, A.W., and Boer de, A. 2005:
Magma Flow through Elastic-Walled Dikes.
*Theor. Comput. Fluid Dyn.*,**19**, 261-286. Simulation Matlab and c-program software for the article. - 14. O. Bokhove, 2005:
- Flooding and drying in finite-element Galerkin discretizations of shallow-water equations. Part I: One dimension.
*J. Sci. Comput.***22**, 47-82. - Flooding and drying in finite-element Galerkin discretizations of shallow-water equations. Part I: One dimension.
- 14b. O. Bokhove, 2004:
- Flooding and drying in finite-element discretizations of shallow-water equations. Part II: two dimensions. Theory of 2D extension.
- 13. O. Bokhove, 2002: Decompressie van magma in opslagtunnels.
*Nederlands Tijdschrift voor Natuurkunde***68**- (
*J. of the Dutch Physics Association*) 232-235. (English translation with technical appendices: ``Decompression of magma into repository tunnels'', with A.W. Woods, Memo. 1654, Math. Comm. 2002 Faculty of Mathematical Sciences, Univ. of Twente, ISSN 0169-2690.) - (
- 12. Andrew W. Woods, Steve Sparks, Onno Bokhove, Anne-Marie Lejeune,
Chuck Connor, and Brittain Hill 2002:
- Modelling magma-drift interaction at the proposed high-level radioactive waste repository at Yucca Mountain, Nevada, USA.
*Geophys. Res. Lett.***29**10.1029.**Download my most famous paper: level 4 on impact** - Modelling magma-drift interaction at the proposed high-level radioactive waste repository at Yucca Mountain, Nevada, USA.
- 12.b O.B. & A. Woods 1999 J. Geophys. Res.
The decompression of basaltic magma into a sub-surface repository, 18 pp.
**Incredible amount of work, but rejected by J. Geophys. Res. because we did not include dynamic solid or rock mechanics.** - In 2008 and 2011 Wout Zweers, Chuck Connor, Koji Kiyosugi and I did such dynamic fluid-rock aka water-gelation
experiments & modelling (incomplete though), including
a tunnel-breakthrough drilled with a starbucks straw:
- - Movie Dike deflects ``magma'' through inclined mine tunnel without nuclear waste

- Movie Dike deflects ``magma'' through mine tunnel without nuclear waste

- Set-up of theory found in IAVCEI presentation

- Movie magma breaking through rock layer, top layer is more stiff;- in 2011, Wout Zweers and I did some extensions (set-up made in 3 days); view from front, and top & left sides -using three 45 degree mirrors .
-**Key issue: nobody did combined modelling & experiment comparison to date because difficult & multidisciplinary (no funding)**? - - Movie Dike deflects ``magma'' through inclined mine tunnel without nuclear waste
- Underlying the GRL publications are a series of very extensive consulting reports for the USA Nuclear Regulatory Committee:

- Two-dimensional Magma-Repository Interactions, 14 pp. ISSN 0169-2690.

- Numerical Modeling of Magma-Repository Interactions, 97 pp. ISSN 0169-2690.

All never published but incredible influential for NRC because I thought the reviewers were right. Bad luck I guess as well as geophysics' politics. - 11. J. Vanneste and O. Bokhove, 2002:
Dirac-bracket aproach to nearly-geostrophic Hamiltonian balanced models.
*Physica D***164**, 152-167

- 10. Onno Bokhove, 2002:
Eulerian variational principles for stratified hydrostatic equations.
*J. Atmos. Sci.***59**, 1619-1628. - 9. Onno Bokhove, 2000: On hydrostatic flows in isentropic coordinates.
*J. Fluid. Mech.***402**, 291-310. - 8. Onno Bokhove and E.R. Johnson, 1999:
- Hybrid Coastal and Interior Modes for Two-Dimensional Flow in a Cylindrical Ocean.
*J. Phys. Ocean.***29**, 93-118. - Hybrid Coastal and Interior Modes for Two-Dimensional Flow in a Cylindrical Ocean.
- 7. Onno Bokhove, 1999: Wiskunde in Weerkunde.
*Ned. Tijds. voor Nat.*(Meteorology and Mathematics.*Journal of the Dutch Physics Association.)*,**65**, 9-13. - 6. Onno Bokhove, Jacques Vanneste, and Thomas Warn, 1998:
- Variational Principle for Barotropic Quasi-Geostrophic Flows.
*Geophys. Astro. Fluid Dyn.*,**88**, 67-79. - Variational Principle for Barotropic Quasi-Geostrophic Flows.
- 5. Bokhove, O., 1997: Slaving principles, balanced dynamics and the Boussinesq equations.
*J. Atmos. Sci.,***54**, 1662-1674. - 4. Bokhove, O. , and T. G. Shepherd, 1996: On Hamiltonian balanced dynamics and the slowest invariant manifold.
*J. Atmos. Sci.,***53**, 276-297. - 3. Warn, T., O. Bokhove, T. G. Shepherd, and G. K. Vallis, 1995:
- Rossby-number expansions, slaving principles and balance dynamics.
*Quart. J. Roy. Meteor. Soc.,***121**, 723-739. - Rossby-number expansions, slaving principles and balance dynamics.
- 2. Bokhove, O. , C. Bruin, and A. Compagner, 1994:
- Ensemble properties and molecular dynamics of unstable systems
*J. Stat. Phys.,***74,**55-73. - Ensemble properties and molecular dynamics of unstable systems
- 1. A. Compagner, C. Bruin, O. Bokhove, 1991:
Molecular dynamics of unstable systems.
*Int. J. of Modern Physics***C2**

- Woods, A.W., S. Sparks, O. Bokhove, A.M. Lejeune, C. Connor, and B. Hill, 1999:
On the motion of magma following the intersection of a dike with a horizontal subsurface tunnel,
*Eos, Transactions of the American Geophysical Union*, 80(46): F1187. - O.B. and Valerie Zwart, 2010: Fluid Fascinations. Qua Art Qua Science brochure, pp. 6. Pdf posted soon. Booklet available upon request till out of stock.
- O.B., Vladimir Molchanov, Marcel Oliver and Bob Peeters 2013:
- On the rate of convergence of the Hamiltonian particle-mesh method.

In: Meshfree Methods for Partial Differential Equations VI (M. Griebel and M.A. Schweitzer, eds.), Lecture Notes in Computational Science and Engineering Vol. 89, Springer, Berlin, 25-43. - On the rate of convergence of the Hamiltonian particle-mesh method.

- S. Legg and K.M.H. Huijts, 2006:
- Preliminary simulations of internal waves and mixing generated by finite amplitude tidal flow over isolated topography.
*Deep Sea Research, part II.***53**, 140-156. Based on practical work Karin Huijts (M.Sc.) at Woods Hole Oceanographic Institution during; Dr. Bokhove strongly stimulated this summer student fellowship with Dr. Legg. 108 citations. - Preliminary simulations of internal waves and mixing generated by finite amplitude tidal flow over isolated topography.
- V.R. Ambati and co-authors 2012:
Port-Hamiltonian discretization for Open Channel Flows.
*Systems and Control Letters.*- Gave advice on time integration and numerical fluxes.
- T. Weinhart, R Hartkamp, AR Thornton, S Luding, Physics of fluids, 2013:
- Coarse-grained local and objective continuum description of three-dimensional granular flows down an inclined surface. 66 citation google scholar;

uses data from and was part of the same research project as my four 2012 granular flow papers. I declined co-authorship, which was accepted with the speed of light, because I could not satisfy (we were moving) the proofreading rule in: Springer's rules. [Mind you nobody is enforcing these rules or codes of conducts, as Springer openly can confirm. Imo such codes of conducts and rules are false advertising.] - Coarse-grained local and objective continuum description of three-dimensional granular flows down an inclined surface. 66 citation google scholar;
- Mercury MD Discrete Element Model by Thornton and Weinhart (2009-2011)
- would not have been build without me stimulating it ab initio, financially via substantial funds (for a Gran Canaria retreat [2011?] from two of my STW projects (on water waves and granular flow), andagainst the wishes of Profs Van der Vegt and Luding, who felt at the time that investing the circa 20k Euros was a waste of money. To date they are still benefitting from my investment and liberal-humanist attitude to stimulating science.
- O.B. & A. Woods 1999 J. Geophys. Res. Rejected.
The decompression of basaltic magma into a sub-surface repository, 18 pp.
**Incredible amount of work, but rejected by J. Geophys. Res. because we did not include dynamic solid or rock mechanics. This is the foundation for our Letter no. 12 so while the letter was accepted the founding work was not; it was of course accepted and heavily scrutinized/reviewed by the USA Nuclear Regulatory Committee. An example of rejected applied mathematics with consequentially no citations that had a heavy influence on policy. Utterly useless in this age of bean counting.**

- 56. Tom Kent, Steve Tobias, O.B. 2017:
- On a non-negativity preserving flux solver for modified shallow models with a rain mass fraction. Note in preparation for a computational journal. See PhD Thesis Tom Kent.
- 57. T. Kent, O. Bokhove, S. Tobias, and G. Inverarity 2017:
- Ensemble Kalman filter data assimilation for a modified shallow water model with convection. In preparation. See PhD Thesis Tom Kent.
- 58. O.B. 2018: On the use of excess flood volume in flood mitigation strategy, for the Boxing Day 2015 Yorkshire floods.
- 59. Anna Kalogirou and O.B. 2018: On variational wave-ship interactions, with a finite-element wave-buoy example.
- 60. Floriane Gidel, T. Bunnik. G. Kapsenberg, Mark Kelmanson, O.B. 2018/2019: Wave-beach interaction in an experiment and numerical wave tank. OMAE 2019 abstract & journal paper.
- 61. O.B., Martin Robinson, Wout Zweers 2017:
- On the Bore-Soliton-Splash and its Relevance to Rogue Waves, Tsunamis and .... In preparation for Nonlinearity.
- W. Kristina, B. van Groesen, and O.B. 2012-2015:
- Effective Coastal Boundary Conditions for Dispersive Tsunami Propagation.

Rejected Theor. Comput. Fluid Dynamics. 20 pp. Submitted July 2012 (review lasted one year; eprint downloaded over 500x so some people are profiting here). Please refer to Chapter 2 of Kristina's PhD Thesis. - Effective Coastal Boundary Conditions for Dispersive Tsunami Propagation.
- Paul Allen, Caroline Shields, Fryderyk Wilczynski, O.B. Chris Jones, Michael Fairweather 2017:
- Optimisation of nozzle port angle in bubbly flows. Subm. & rejected 28-03 Metallurgical and Materials Trans. B.
- Tunuguntla et al. 2016-2018:
- Granular flows in inclined channels with a linear contraction. Still in preparation

- Bokhove, Slaved Hamiltonian method a.o.

- 1. Bokhove, O. and A. Compagner, 1990: One-dimensional collapse.
In:
*Computational Physics and Cellular Automata*(A. Pires, D. P Landau and H. Herrmann, eds.), World Scientific, Singapore, 179-182. - 2. Onno Bokhove, 2002:
*Balanced models in Geophysical Fluid Dynamics: Hamiltonian formulation, constraints and formal stability.*CUP-online excerpt*(old draft online)*Chapter 1, 63 pp., in ``Large-Scale Atmosphere-Ocean Dynamics 2, geometric Methods and Models''. Editted by J. Norbury and I. Roulstone, Cambridge University Press. 364 pp, ISBN: 0521807573. - 3. O. Bokhove, and D. Wirosoetisno, 2004: Drying and wetting in finite element shallow-water flows
In:
*Shallow Flows*Research presented at the International Symposium on Shallow Flows, Delft, Netherlands, 2003 Eds. Gerhard H. Jirka and Wim S. J. Uijttewaal, Balkema Publishers. ISBN: 9058097005, 601-608. - 4. O. Bokhove, 2005: Wave-vortex interactions in the atmosphere, and climate prediction. (Preprint.) Official version Proceedings of the ICTAM04 Conference in Warsaw, Poland, Publisher: IPPT PAN, Warsaw 2004, ISBN: 83-89687-01-1, Eds. Witold Gutkowski and Tomasz Kowalewski, 103-116.
- 5. O. Bokhove and A.R. Thornton 2012: Shallow granular flows. Chapter in Handbook of Environmental Fluid Dynamics.

Editor: Joe Fernando; Taylor and Francis.

- Bokhove, O., 1990:
*Veeldeeltjessystemen met Vereenvoudigde Gravitatiepotentialen.*(Many-particle systems with simplified gravitational potentials.), M.Sc. Thesis. Delft University of Technology, 77 pp. - Bokhove, O., 1996:
*On balanced models in Geophysical Fluid Dynamics:**slowest invariant manifolds, slaving principles, and Hamiltonian Structure:*Ph.D. Dissertation. University of Toronto, 186 pp.

Veluwe Rally 100km River IJssel: 7:07 (2:58) 2007 [6:55 (3:00) 2006 (7hrs 6min (3:00) 2005; 7hrs 21min, 2004; 6hrs 51min in 2002; ~20min=2x10min rest]

- (vi) Profs Bokhove/Tobias NERC DTP PhD Position with UK Met Office, Drs Bell, Inverarity and Migliorini.
- (v) Various open PhD positions in our new EPSRC Fluid Dynamics Centre at Leeds, in collaboration with HR Wallingford (hydraulic research), EDF France/UK (hydraulics research), Tata Steel (Teesside), MTI Holland (dredging research), Netherlands Institute for Sea Research (Prof. Maas), Chemical Engineering University of Eindhoven (prof. Kuipers), Physics of Fluids Group University of Twente (Prof. Van der Meer).
- (iv) Research Assistant (postdoc), Anna Kalogirou, 2014.
- (ii, iii) EU European Industry Doctorate: two ESRs/PhDs Floriane Gidel/Tomasz Salwa, 2014.
- (i) EPSRC CASE on "Data Assimilation for Idealised Mathematical Models of Weather Prediction"
with the Met. Office. 2013-2016. PhD: Tom Kent.

- 4. B. van Groesen with Onno Bokhove and Andonowati 2007-06-07 Nearshore tsunami modelling and simulation. NWO ALW. Approved. Ph.D.: Wenny Kristina 2008-2012.
- 3. O. Bokhove and J.J.W. van der Vegt 2007-05-16 A numerical wave tank for complex wave and current interactions, Proposal to STW, Dutch Engineering council. Approved Dec. 2007. PhD: Shavarsh Nurijanyan 2009-2012. Postdoc: Vijaya Ambati.
- 2. O. Bokhove and J.J.W. van der Vegt 2008 Compatible mathematical models for coastal hydrodynamics. Awarded. NWO EW-proposal 15-01-2008. PhD: Elena Gagarina.
- 1. "Polydispersed granular flow through inclined channels -influence of particle characteristics, channel rotation and geometry"

STW/Neth. Eng. Res. Council with users: Corus, Unilever, BASF; four university groups from UT and TUe. PI. Approved 2010. PhD: DT.

My supervision was interrupted because I disagree, cf. multiple ethics codes including the one cited above and below, with submission of manuscripts to journals or archives before all co-authors have been asked for and have given consent. This concerned: (I) 1 JFM submission published in 2014 (in which I had to intervene through the editor to fix several mistakes including 1 big simulation error) and II) 1 archive submission (in which 2 of the 4 co-authors have never been asked for approval). I had written the STW proposal in 2007-2008 after a successful and nice collaboration with Prof Hans Kuipers (TUe) in 2006-2010. My (informal) requests for moderation were dismissed and/or ignored (at both provincial and national levels).**The conclusion is that ethics' codes exist only for show, not for content. See the essay ``Scrofulous'' at the bottom of the page**

with an appendix ``Slaved Hamiltonian dynamics'' by O. Bokhove and T.G. Shepherd. 21 pp. Notes.

In 2007 I developed a marvelous interdisciplinary collaboration on granular flows with Prof Hans Kuipers, who left the University of Twente around 2010 while I left in 2013. Disagreement about the management directions were the main reasons to leave including, for me, scrofulous behavior that continues to date.

(i) In general, the amount of editting required is underestimated by juniors and some supervisors. E.g. for (I), there were about 6 to 10 iterations required from the 1st iteration with circa 100 comments on Dec. 12th 2013 till the last iteration on Dec. 23rd 2013 (to be quite honest doing this just before Xmas at a workshop was outrageous but the editor had given us 14 days to resolve matters). Notice how the oscillations in Fig. 2 have disappeared in the final version because the resolution was increased and a computational error was found during the editting process. Making double-resolution runs to verify convergence was dismissed as a time waste and I was asked by the supervising professor to leave as co-author of this paper. That loud request was made before regarding another paper in 2012, another paper in 2013, in 2014 and has recently been made again for yet another paper --see below. [Fixing these errors is not urgent according to some people as the results are "kind of" the same and one can always publish the correct figure in a new publication, thus boosting one's publication and citation records. I don't belong to the group of people advocating that kind of philosophy. The (Dutch) academic system does, however, award this kind of behaviour of quantity above quality. It thrashes people who advocate quality.] One reviewer congratulated us in the end for a well-written and impactful paper. The dean of the said faculty dismissed it all as fixing typos because it delayed the process (by two weeks) and because seniors such as the dean and the prof above, dismiss(ed) careful editting as mistrusting other people (I always triple-check my own work, let it be the work of others, especially juniors who need to learn the trade, and so do my Leeds and Imperial mathematics' colleagues).

(ia) As said, it is not the first time that sloppy science causes mishaps. In 2012, I turned down authorship of a paper since it contained too many copied sentences of four of our joint papers. Such copying first of all leads to a poorly written paper and, second, it is self-plagiarising and after I declined, plagiarism. In addition, I had asked to not mention the specific idea to couple DEM to hpGEM, an idea that I had proposed and advocated in the STW-proposal, which I wrote for 95% as PI. Given my move to Leeds and also given the more stringent clamp-down on plagiarism in the UK, as opposed to The Netherlands, and rightly so, I did not want to get involved in self-plagiarising. The authors refused to clean up their act and mentioned ideas I had proposed and advocated without reference to me in relation to the STW-proposal. They also did not acknowledge that I had given them my suggestions for improvement, which they did use. Relative to the first draft the final paper indeed had greatly improved ---they should have asked me to rejoin again as co-author, which they did not, thus plagiarising my ideas without acknowledgment. Such Trumpian-bully style tactics are standard in that university and apparently allowed by the Dutch funding agency STW-NWO. My complaint at STW-NWO was cleverly and incorrectly circumvented and led back to me, thus avoiding STW to take responsibility: as project leader I was forced to sign a STW project-form effectively stating "the project leader confirms that all research complies with the Dutch scientific ethics laws". I refused to do so, as that was not the case, and raised my complaint, in vain. Poor leadership on the part of STW which ultimately led to the approval of a PhD thesis with a provably incorrect chapter, in which calculations need to be redone --see point ii). Apparently, approval of an incorrect PhD thesis (chapter) is allowed in The Netherlands and by funding agency STW-NWO. Given the history, STW could have known that sloppy science was likely to happen again. Hence, they cannot use the "ich-habe-es-nicht-gewusst" excuse as I had flagged the issue with several of their employees including the former director (now an MP on education). One STW employee supported my complaint but warned me that I was likely to lose since the dean of the faculty was a member of STW's advisory board; he expected my character assassination given that I was not physically present full-time in The Netherlands to defend myself---this is indeed what happened; "group dynamics against the person who cannot defend himself", was a friend's analysis and: "a common trick". It still does not allow STW-NWO or any other management to approve of plagiarism, ghost authorship, and stealing of shared ideas combined with agressive attempts (4x by the same senior prof) to bully a key author in an attempt to make him withdraw as author for the wrong reasons. Apparently in The Netherlands this all is allowed, which is why I defected the country. Organised Dutch science, like organised crime, is at fault here, notwithstanding that I know and collaborate with plenty of bonafide scientists in The Netherlands.

(ii) On (II), this manuscript found in the archive here was deposited while neither co-author Thomas Weinhart nor I were given the opportunity to proofread and make corrections. The archive also refused to delete the deposited manuscript given that our names are illegally attached. My comments were finally asked late Nov 2016 and the manuscript (essentially an approved PhD thesis chapter --how on Earth did this pass the PhD committee? --I was not involved) with my 172 minor and major comments is found here; I also rewrote one subsection later (not shown) as it copied a part of the published Akers and Bokhove 2008 article (Phys. Fluids) too much. Some serious corrections are required; attempts to correct came seven months later, see (v) below. These are facts, as you can check yourself given the interim manuscripts, not alt-facts the latter aka typos, errors-declared-no-errors, minor quibbles, etc. My main point of critique was actually raised at the PhD defence, I was told by one of the committee members, but the incorrect write-up was defended as another and apparently acceptable alternative (fact), aka ``Dutch science''. [With minor defensive writing, by admitting the mistake and outlining its correction, the current write-up could have been augmented, so a practical correction would have been trivial way to set matters right.]

(iii) I have the opinion that the PhD student has been a victim of inadequate supervision and that he therefore should be allowed to correct the erroneous chapter in his online PhD thesis. It is unprofessional (otherwise said simply sickening) that the collective formal supervisory team of this junior researcher at that university was unwilling to provide serious and constructive comments fixing the minor and major errors in the four manuscripts/iterations to date (two archived manuscripts, a thesis chapter and two draft journal articles). This correctional procedure should be checked by an independent, ad-hoc (PhD) committee of two esteemed scientists who should oversee the corrections as (remote) reviewers. Substance should go before old-fashioned Dutch customs. That is unlikely to happen as not loosing face is deemed more important than maintaining quality and substance, a difference of principles that lies at the heart of the matter. Is that Dutch academics in a nutshell? As external I recently proofread a draft thesis in the UK. On page 2 of that UK thesis, now approved by me, the following statement emerges: "I cerify that this thesis is the product of my pwn work, and that any ideas or quotations from the work of other people, published or otherwise, are properly acknowledged". Regarding the chapter in the approved 2015 PhD thesis on granular flow through a contraction that statement does not apply. That I defined the problem as PI of the proposal, that I set up and shared the detailed calculations with the PhD student and one of the authors in 2010-2012, that I pointed out that the shallow water and DEM calculations could principally not be that different (already pointed out in 2012) and that I pointed out further errors in the 2014 archived manuscript, has not been acknowledged in the PhD thesis. The incorrect reference in the thesis gives the impression that 2 or 4 supervisors are jointly responsible for the intelllectual content of that chapter. The addition of 2 or 3 professors --including me-- afterwards, in the draft article, gives the incorrect impression that I am an add-on, which I am not. Till 2014, I was always last author in the draft article as mentioned in the minutes of many STW meetings. I am not a ghost author, a well-defined phrase in academic publishing, namely an author who should not be co-author on an article because he/she does not satisfy the four rules on authorship below in (vi); quite the contrary, I am one of the lead authors, the one who defined this research before anyone else was involved.

(iv) Just to be clear why I have taken the unusual step to place matters openly online: I have given university and funding agency ample opportunities (2012-2016) to solve these matters behind closed doors. They refused at all levels. Defending my right and the general scientific principle that errors should be fixed and that all authors should be asked for permission (to submit to a journal or archive), against all odds and certainly when feasible corrections are known, which was the case as I have always provided such corrections promptly, cost me personally 6000 euros in legal fees. It concerned four articles, two of which have been considered for submission as Level 4 Research-Excellence-Framework papers. Without my insistence to correct errors the latter REF-papers would have a lower rating. In addition, ``driemaal is scheeprecht'' (three times is enough --a Dutch saying), a prof for the third time asked me to withdraw as co-author on a third (journal) paper, while criticising my so-called high standards, i.e. the fact that I actually proofread draft work a few times, while he admits to simply ``trust'' the word of juniors that the corrections are done. Well, I am finally and openly fed up with such unprofessional behaviour; it is not happening in my backyard. The cynical question is whether such behaviour is unprofessional or not: from the point of view of maximising the number of PhD theses supervised and the number of journal articles published the said prof is a top professional and my insistence on quality (for corrections feasible within the time span of a few weeks) is simply unprofessional (aka stupid), given that the (Dutch) academic system awards quantity above quality. It thrashes -de facto- people like me, both at the funding agency (NWO/STW) as well as the university levels. Remember Arthur Gotlieb? Apparently, the only defense a scientist has when incomplete and incorrect work based on his input is placed online and cannot be removed, is to place the critical and constructive comments on this research online. Normally such corrections are done behind the scene and that is preferred, of course. But if the scientist is attacked and threatened with being fired, for insisting on sensible and manageable corrections, he or she has no other choice than go public. [Update 28-09: finally one other senior co-author proofread carefully; that took him apparently and unexpectedly 3 weekends; join my UK academic world as proofreading indeed takes time. Update 01-12: after highlighting that matters are still not resolved, I got an update back. TBC.]

(v) Reading the new draft, page by page. 18-08-2017: on page 8, hitherto 95 comments (as of 19-08: 100 comments); ... I will continue my careful proofreading probably later this autumn (I spent one week proofreading a UK thesis as external reviewer, which should be the normal state of affairs but in an altfacting world of one-liners and quick fixes has become the anti-norm, and had two weeks of holidays in Aug/Sept). Meanwhile I have been accused that my standards are too high by a prof who strongly suggested me to leave as author (for the fourth time since 2012). Whatever my standards are, what is relevant is that the science needs to be fine, that e.g. the following needed and needs to be corrected:

- The basic mistake in the Dec 2016 draft remains unsolved: a very thin channel has been taken, as thin as the inflowing layer with only a short contraction, and this does violate the shallow flow assumptions made. The issue is not that a junior makes an error, we all make errors, but the issue is the refusal to find these errors by careful proofreading by the official supervisors and the dismissal of obvious errors as "high standards" beyond reach of correction, plus the subsequent attempt to get rid of the person finding the errors and suggesting the corrections to these errors. Instead, I have been asked to withdraw as co-author, whereafter they would undoubtedly fix the errors I pointed out ---this happened with a paper in 2012 in which my contributions were not acknowledged. In this case my contributions are much more profound. The actual corrections are a week to two weeks worth of work --that is all.

- More technically, the basic scaling error that tan(theta) = [tan(theta)]' times H/W with H a different layer thickness length scale than channel width W is suboptimal to say the least. The prime means that [tan(theta)] was scaled. Well, an angle is dimensionless and so is the tangent so it cannot be made dimensionless as it already is dimensionaless. Now as adviced by me, H=L is taken but the in-plane scale L cannot equal to W otherwise the flow is not shallow (a mistake likely present in this new draft). See expression (2.3) in the 2016 draft with my comments and the thesis, etc.

- Except that taking the upstream depth scale H also as width and downstream length scales in combination with the shallowness assumption implies that the width of the channel should be "many" depth scales H (e.g, 5H, 10H or more or many more particle diameters?) and that the channel constriction length should be a multiple of the width (e.g., 20H, 40H or more?). After all, the 1D but also 2D models are based on asymptotics. I am doubtful whether the plots displayed take into account this necessity to keep width and downstream scales very long?

- So despite the correction of the formal scaling, due to the use of a domain that is too narrow and a contraction that is too short, the previous lack of agreement between shallow water theory and discrete particle simulations is still suboptimal, to say the least. Nonetheless, it is ambiguously described in the 2017 draft text to be both as "close agreement could not be reached" as well as "i.e. the flow profiles in the contraction did not completely match the one-dimensional predictions"; as said, there likely still is an issue regarding the shallowness induced by the channel width and downstream contraction length scales used; the problem is that these statements are unclear if not mutually exclusive; "not completely match" meaning that the agreement is close which is not in agreement with the first statement that "close agreement could not be reached"; I prefer precise languange to be used as well as correct shallow flow and DEM simulations to be performed with clear scale markers to be added in the article, to celebrate a possibly joint victory, credited to us all.

- In the 2017 draft the 2D oblique shocks are described as being smooth. They are not. Shocks are by definition not smooth. The point is that the width-average of these oblique shocks is smooth. Well, then say so. Clarity matters.

- A hydraulic set-up in another article (Akers and Bokhove 2008) was called the same as these inclined channel calculations while the hydraulic channel was in fact horizontal, meaning not inclined. I know as I did 50% of these experiments. Then say so. Clarity matters.

I prefer all such things to be presented truthfully and consider it as an integral part of publishing to eliminate nearly all misrepresentations and errors, within the reach of a few careful rounds of proofreading. This is only round two of proofreading of full drafts (of 2016 and 2017 as the 2014 archived draft I just browsed while spotting several mistakes within the span of 15 minutes). Two rounds of proofreading is not very much, by the way. I object to careless or no proofreading. Dutch organised science (as opposed to Dutch scientists) does, apparently and till proven otherwise, not care about careful science but awards sloppy science. That sloppy science and altfacting is likely commonplace in (Dutch) science is argued here by Prof Lex Bouter and in my wordpress blog article Hypocratie van alternatieve en voldongen feiten in de Nederlandse wetenschap.

(vi) Finally, this is what Springer (first link to this clear set of rules) recommends [I am on the editorial board of a Springer journal so ought to know and follow this]:

"The ICMJE recommends that authorship be based on the following 4 criteria:

1. Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND

2. Drafting the work or revising it critically for important intellectual content; AND

3. Final approval of the version to be published; AND

4. Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Contributors who meet fewer than all 4 of the above criteria for authorship should not be listed as authors, but they should be acknowledged. "

What a relief. I ticked all four boxes, i.e., I should be co-author according to (Springer) standards which nobody is upholding in a world where only the number of papers published and citations count! To wit: 1. The intellectual design is mine since I led and wrote 95% of the STW proposal plus set up/shared my (hand-written and blackboard) calculations; 2. for sure I drafted the work and my standards are not disputed, apparently, instead my standards are deemed too high; 3. my approval is obviously not yet given but matters are coming along; and, 4. for sure, I am clearly accountable as follows from my proofreading and checking, which should be standard practice by any professional academic. Wow, that's great. Tough but fair requirements though. Unfortunately, Springer or publishers in general do not let their editors sign a contract stating explicitly that they will follow these rules in their own scientific practice, all of them, not on a voluntary basis. Only when there is a signature can there be repercussions. My standards are normal by the way: in the above July 2017 draft version reference to the 2015 PhD thesis has been removed since referencing a thesis chapter with errors was deemed unwise, i.e., they implicitly admit themselves that the standard of the thesis chapter was too low. The suggestion by this senior prof that my standards are too high are nothing less than an attempt to claim that the high standards are his and not mine. It is a dirty trick, tried for the fourth time for a fourth article which, my dear friends would say, is apparently perfectly allowable in the Dutch academic setting, unless proven otherwise. "Dutch science", till proven otherwise, a close friend has called it, like "Dutch wife", "Dutch courage" and such.

(vii) The above is a scientific discourse. Recall that I paid a lawyer 6000 euros in the period 2013-2015 to defend my author's rights and my right to do exactly what Springer refers to in the point 4. above: "to be accountable for all aspects of the [ie my] work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved", as well teach junior researchers to do so. Those rights were and probably are still under threat in the current (Dutch) scientific climate. (In 2013 concerning a different junior, after approval of a manuscript by the reviewers of a high-ranking journal, I found a serious error. I asked the editor of that journal whether we could have one extra month and later another month, for us to fix the error. We added an extra appendix with permission of the editor. This was a tough learning experience for the, excellent, junior. When the page proofs of the article arrived, my wife and I took the junior and partner out for dinner in our old home town (Enschede), our treat, of course, to celebrate victory after all this extremely hard work. That was an act of empathy.)

(viii) Every Thursday (in term time) my research group of PhDs and PDRA's has a group meeting in which we in turn listen to informal research presentations. This also includes try-outs for formal presentations and discussions on research obstacles. Afterwards we go for lunch. Often I don't have to say much as the group has the answers to most questions and the group picks up the weak points in presentations. These are training sessions for all "ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved". Late April 2015, my group picked my draft public outreach presentation which I had prepared completely apart. I had asked them to comment, admitting beforehand that I was stuck in trying to deliver my message to the general public. That must have been amusing for them to pick their supervisor's trial presentation apart. They showed no mercy in a polite but clear manner and, in effect, did show actual as oppposed to surperficial mercy, since the factual public presentation would otherwise have been of lesser quality. Constructive yet firm criticism is crucial for making progress. (A significant subset of the senior co-authors in the above papers on granular flows does understand this very well, of course, but want(ed) to get rid of me as co-author so they can claim my contributions as their own. Recall that one of ``them'' profs actively suggest(ed) I leave the paper on which I should be co-authored according to all Springer authorship's rules cited above. Such agressive attempts to get rid of authors is likely a common tactic in science.) Afterwards we had our (nice) weekly group lunch and the subsequent Sunday in Hebden Bridge I gave a well-received presentation on the science of flooding. The School of Maths has discussed the option to create more of these small-scale group meetings within the School to enhance the research atmosphere. During my PhD study in Toronto under the supervision of FRS Prof Ted Shepherd such informal group meetings, followed by a lunch in China Town (``rice with beef and black bean sauce'' was my favourite), were the norm. The apple does not fall far from the tree.

Email: O.Bokhove TE maths.leeds.ac.uk