In all my papers I (try to) follow the ethics of a journal such as Physics of Fluids, say. "When an error is discovered in a published work, it is the obligation of all authors to promptly retract the paper or correct the results." and "All coauthors have an obligation to provide prompt retractions or correction of errors in published works. Any individual unwilling or unable to accept appropriate responsibility for a paper should not be a coauthor."
- 55. Salwa, Bokhove, Kelmanson 2017:
- Variational modelling of wave-structure interactions with an offshore wind-turbine mast.
In press 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.
- 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
- 51. A. Kalogirou, E.E. Moulopoulou, O.B. 2016:
- Variational finite element method for Waves in a Hele-Shaw Tank. Appl. Math. Modelling.
- 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).
- 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.
- 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
- 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. preprint
- 46. E. Gagarina, V.R. Ambati, J van der Vegt and O.B. 2014:
DGFEM for nonlinear free surface waves. J. Comp Phys. 275, 459-483.
Preversion 2008: eprints.
- 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.
- 44. S. Nurijanyan, O.B. and L.R.M. Maas 2013:
Inertial waves in a cuboid. Note on series solutions.
Phys. Fluids 25 126601
- 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.
- 42. S. Nurijanyan, J.J.W. van der Vegt, O.B. 2013:
- Hamiltonian DGFEM for rotating linear incompressible Euler equations: inertial waves.
J. Comp. Phys. 241, 502-525
- 41. Thornton, Weinhart, Luding, B. 2012:
Frictional dependence of shallow granular flows from particle simulations.
- Eur. Phys. J. 35, 127. eprints.
- 40. Thornton, Weinhart, Luding, B. 2012:
Modelling of particle size segregation: calibration using the discrete particle method.
- Int. J. Mod. Phys. C. 23, 1240014. eprints
- 39. Weinhart, Thornton, Luding, B. 2012:
- From granular particles to continuum fields near a bounday.
Special Issue. Granular Matter 14, 289-294.
- 38. Weinhart, Thornton, Luding, B. 2012:
Closure relations for shallow granular flows from particle simulations.
Granular Matter 14, 531-552. eprints.
- 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
- 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.
- 34. O. Bokhove and Marcel Oliver 2009:
- Hamiltonian N layer model for atmospheric dynamics. (memo 2008) Geophys. Astrophys. Fluid Dyn. 103(6), 423-442.
- 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.
- 31. Ben Akers and Onno Bokhove, 2008:
Hydraulic flow through a contraction: multiple steady states.
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.
Based on a Finite Volume exercise vi of Bokhove in the course (2005) numerical techniques for PDE's.
- 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.
- 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.
- 27. V.R. Ambati and O. Bokhove, 2007:
. J. Comp. Phys. 225, 1233-1261.
- Space-time discontinuous Galerkin discretization of rotating shallow water
- 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.
- 25. Bokhove, O. and P. Lynch 2007:
Air parcel and air particles: Hamiltonian dynamics.
Nieuw Archief voor Wiskunde 5, 100-106.
- (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
- hpGEM- A software framework for Discontinuous Galerkin finite element methods,
ACM Transactions on Software 33 (4). eprints.
- 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: Vreman et al.
and also Memo. 1788, Math. Comm. Dept. of Applied Math. 2005, Univ. of Twente. ISSN 0169-2690
- 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.
- 21. V.R. Ambati and O. Bokhove, 2007:
Space-time finite element shallow water flows. J. Comp. Appl. Math.
204 (2), 452-462.
- 20. E. Bernsen, O. Bokhove, and D. van der Sar, 2006: Numerical prediction of rose growth.
Acta Horticulturae. 718, 89-96.
- Memo. 1803 with appendices.
- 19. Bokhove, O. and Oliver, M. 2006: Parcel Eulerian-Lagrangian fluid dynamics for rotating geophysical flows.
- Proc. Roy. Soc. A. 462, 2575-2592,
- 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.
- 17. Woods, A.W., Bokhove, O., Boer de, A., Hill, B.E. 2006:
- Compressible magma flow in a two-dimensional elastic-walled conduit
(proofs). Earth Planet. Sci. Lett. 246, 241-250.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.,
- 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.,
- 2. Bokhove, O. , C. Bruin, and A. Compagner, 1994:
- Ensemble properties and molecular dynamics of unstable systems, J. Stat. Phys., 74, 55-73.
- 1. A. Compagner, C. Bruin, O. Bokhove, 1991:
Molecular dynamics of unstable systems. Int. J. of Modern Physics
Publications (former) researchers while in my group
- 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.
- 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
- 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.
Chapters and selected contributions in books
- 56. Paul Allen, Caroline Shields, Fryderyk Wilczynski, O.B. Chris Jones, Michael Fairweather 2017:
Optimisation of nozzle port angle in bubbly flows. Subm. 28-03 Metallurgical and Materials Trans. B.
- 57. Oers, Bokhove, Maas 2017:
- Hamiltonian formulation of nonlinear and linear incompressible (Boussinesq) equations.
Note in preparation for, e.g., J. Fluid Mech.
- 58. 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.
- 59. 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.
- 60. O.B., Martin Robinson, Wout Zweers 2017:
On the Bore-Soliton-Splash and its Relevance to Rogue Waves, Tsunamis and ....
In preparation for Nonlinearity.
- 61. 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.
- - Tunuguntla et al. 2017:
- Granular flows in inclined channels with a linear contraction. Revision stalled.
- 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.
(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]
Bokhove, O., 1993: On Hamiltonian balanced models. In: Ninth A. M. S.
Conference Proceedings on Atmospheric and Oceanic Waves and Stability
Bokhove, O., T. Warn, T. G. Shepherd, and G. K. Vallis, 1995: Rossby-number
Expansions, slaving principles, and balance dynamics. In: Tenth A.M. S
Conference Proceedings on Atmospheric and Oceanic Waves and Stability. 268-269.
O. Bokhove and E.R. Johnson, 1997:
On hybrid beta-plane Rossby and topographic shelf modes.
In: Eleventh A.M.S.
Conference Proceedings on Atmospheric and Oceanic Fluid Dynamics. 206-207.
D.H. Peregrine and O. Bokhove, 1998:
Vorticity and surf zone currents. In: 26th International
Conference on Coastal Engineering, Reston ASCE, Copenhagen. 745-758,
Ed. Billy. L. Edge, ISBN: 0-7844-0411-9.
O. Bokhove, 1999:
Forced-dissipative response for coupled planetary Rossby and
topographic shelf modes in homogeneous, cylindrical oceans.
In: Twelfth A.M.S.
Conference Proceedings on Atmospheric and Oceanic Fluid Dynamics.
O. Bokhove and D.H. Peregrine, 1999:
The generation of longshore currents and
eddies by breaking waves
in the surf zone.
In: Twelfth A.M.S.
on Atmospheric and Oceanic Fluid Dynamics.
O. Bokhove, M.D. Patterson, and D.H. Peregrine, 2000:
Breaking shallow water wave simulations in
the surf and swash zone. In: 27th International
Conference on Coastal Engineering, Reston ASCE, Sydney,
Ed. Billy L. Edge, ISBN: 0-7844-0549-2.
Jan Bouwe van den Berg, Onno Bokhove, Mark Peletier, JF Williams,
and Hans Zwart, 2001:
Thermal modeling in polymer extrusion.
Refereed Proceedings of the 39th European Study Group
with Industry at the University of Twente.
Eds. B.W. van de Fliert and G. Meinsma. 57-67, ISBN 90 423 0132 5.
Bokhove, O., Getto, P.H., 't Hof, B. van, Dubbeldam, J., Ovenden, N., Pik, D., Prokert, G.,
Rottschafer, V., and Sar van der, D.M., 2002:
Roses are unselfish: a greenhouse growth model to predict harvest rates.
Refereed Proceedings of the 42nd European Study Group with
Industry at the University of Amsterdam, 59-76.
O. Bokhove, and D. Wirosoetisno, 2003:
Drying and wetting in finite element shallow-water flows
In: International Symposium on Shallow Flows
June 16-18 2003, Delft University of Technology, The Netherlands ,
Ed. Gerhard H. Jirka and Wim S. J. Uijttewaal, 153-160.
Bernsen, E., Bokhove, O., and J.J.W. van der Vegt 2006:
A (dis)continuous finite element model for
generalized 2D vorticity dynamics. Eccomas paper.
European Conference on Computational Fluid Dynamics.
Bokhove, O. (joint work with Marcel Oliver) 2006:
Spherical Hamiltonian 2-layer model for atmospheric dynamics.
In: Mathematical Theory and Modelling in Atmosphere-Ocean Science.
Mathematisches Forschungs Institut Oberwolfach, Eds: Buhler, Majda, Klein,
Oberwolfach Reports 3 (3) 2369-2372.
A. Stoorvogel et al. 2008:
Math Fights Flooding Proceedings Study Group Mathematics with Industry 2008, also co-editor.
- (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.
(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 maths colleagues).
(ia) This is not the first time this happened. In 2012, I turned down authorship of a paper since it contained too many copied sentences of 4 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 TBD, 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 TBD. They also did not acknowledge that I had given them my suggestions for improvement. Relative to the first draft the final paper TBD 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 an 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 a 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 bonafied 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 Akers and Bokhove 2008 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.
(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 4 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. On page 2 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 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 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 mentioned in the minutes of the STW meetings. I am not a ghost author, a well-defined phrase in academic publishing, namely an author who
should not been co-author on an article because he/she does not satisfy the 4 rules below in (vi), quite the contrary.
(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 these 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 in scheeprecht (3 times is enough), a prof for the third time asked me to withdraw as co-author on a yet third (journal) paper
criticising my 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.
(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 early Oct (I spent one week proof reading 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 have two weeks of holidays).
Meanwhile I have been accused that my standards are too high by a prof who strongly suggested me to leave as author (for the 4th 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 the 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?) 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 model is 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 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"; but 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 and correct shallow flow and DEM simulations 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 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 2 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 and in my wordpress blog article "Hypocratie van alternatieve en voldongen feiten in de Nederlandse wetenschap".
(vi) Finally, this is what Springer 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 proposal plus set up/shared my calculations; 2. for sure I drafted the work and my standards are not disputed, apparently, instead my standards are deemed to 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 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 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 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 4th time for a 4th 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 from 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.
(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 a draft public outreach presentation 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 mercy, since the actual 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 do understand this very well, of course, but want to get rid of me as co-author so they can claim my contributions as their own. Recall that one of them profs actively suggests I leave a 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 a nice 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.
Reports and Memoranda
W.E.H. Sollie, J.J.W. van der Vegt, and O. Bokhove 2006:
A space discontinuous Galerkin finite element method for two-fluids problems. Part I: Theory.
Part II. Verification. See eprints. Memo.
O. Bokhove 2007:
Constrained 1.5-Layer Model for Troposphere-Stratosphere dynamics.
with an appendix ``Slaved Hamiltonian dynamics'' by O. Bokhove and T.G. Shepherd. 21 pp. Notes.
O. Bokhove, 2003:
Flooding and drying in finite-element discretizations of shallow-water equations.
Part II: two dimensions.
Mathematical Communications 2003 University of Twente 1684, 21 pp.
O. Bokhove, 2003: Flooding and drying in finite-element
discretizations of shallow-water equations.
Mathematical Communications 2003 University of Twente, memorandum 1683.
O. Bokhove, T.G. Shepherd, and D. Wirosoetisno 2003:
Hamiltonian Wave-Vortex and Vortex Models.
Manuscript 12 pp, memorandum in preparation.
O. Bokhove and A.W. Woods, 2002
Decompression of magma into repository tunnels.
The Mathematical Communications
of the Faculty of Mathematical Sciences, University of Twente, ISSN 0169-2690
Bokhove, O. and Woods, A.W., 2002:
The decompression of basaltic magma into a sub-surface repository, 18 pp.
Memorandum 1616 in The Mathematical Communications 2002
of the Faculty of Mathematical Sciences, University of Twente, ISSN 0169-2690.
Andrew W. Woods, Steve Sparks, Onno Bokhove, Anne-Marie Lejeune,
Chuck Connor, and Brittain Hill 2001:
Modelling the explosive eruption of basaltic magma into
the proposed high level radioactive waste repository
at Yucca Mountain, Nevada. Refereed report for the Nuclear Regulatory Commission, 18 pp
Interim Milestone IM 20.01402.461.115, http://www.ymp.gov.
Onno Bokhove, 2001:
Two-dimensional Magma-Repository Interactions, 14 pp.
in The Mathematical Communications 2001
of the Faculty of Mathematical Sciences, University of Twente, ISSN 0169-2690.
Onno Bokhove, 2001:
Numerical Modeling of Magma-Repository Interactions, 97 pp.
in The Mathematical Communications 2001
of the Faculty of Mathematical Sciences, University of Twente, ISSN 0169-2690.
Bokhove, O. and Woods, A.W., 2000:
Explosive Magma-Air Interactions by Volatile-Rich
Basaltic Melts in a Dike-Drift Geometry.
Refereed report prepared for the Nuclear Regulatory Commission, Washington U.S.A., 55 pp,
Interim mile stone IM 1402.461.040, http://www.ymp.gov.
Email: O.Bokhove TE maths.leeds.ac.uk|