66 research outputs found
Numerical wave propagation for the triangular - finite element pair
Inertia-gravity mode and Rossby mode dispersion properties are examined for
discretisations of the linearized rotating shallow-water equations using the
- finite element pair on arbitrary triangulations in planar
geometry. A discrete Helmholtz decomposition of the functions in the velocity
space based on potentials taken from the pressure space is used to provide a
complete description of the numerical wave propagation for the discretised
equations. In the -plane case, this decomposition is used to obtain
decoupled equations for the geostrophic modes, the inertia-gravity modes, and
the inertial oscillations. As has been noticed previously, the geostrophic
modes are steady. The Helmholtz decomposition is used to show that the
resulting inertia-gravity wave equation is third-order accurate in space. In
general the \pdgp finite element pair is second-order accurate, so this leads
to very accurate wave propagation. It is further shown that the only spurious
modes supported by this discretisation are spurious inertial oscillations which
have frequency , and which do not propagate. The Helmholtz decomposition
also allows a simple derivation of the quasi-geostrophic limit of the
discretised - equations in the -plane case, resulting in a
Rossby wave equation which is also third-order accurate.Comment: Revised version prior to final journal submissio
Diagnostic tools for 3D unstructured oceanographic data
Most ocean models in current use are built upon structured meshes. It follows
that most existing tools for extracting diagnostic quantities (volume and
surface integrals, for example) from ocean model output are constructed using
techniques and software tools which assume structured meshes. The greater
complexity inherent in unstructured meshes (especially fully unstructured grids
which are unstructured in the vertical as well as the horizontal direction) has
left some oceanographers, accustomed to traditional methods, unclear on how to
calculate diagnostics on these meshes. In this paper we show that tools for
extracting diagnostic data from the new generation of unstructured ocean models
can be constructed with relative ease using open source software. Higher level
languages such as Python, in conjunction with packages such as NumPy, SciPy,
VTK and MayaVi, provide many of the high-level primitives needed to perform 3D
visualisation and evaluate diagnostic quantities, e.g. density fluxes. We
demonstrate this in the particular case of calculating flux of vector fields
through isosurfaces, using flow data obtained from the unstructured mesh finite
element ocean code ICOM, however this tool can be applied to model output from
any unstructured grid ocean code
Mixed finite elements for numerical weather prediction
We show how two-dimensional mixed finite element methods that satisfy the
conditions of finite element exterior calculus can be used for the horizontal
discretisation of dynamical cores for numerical weather prediction on
pseudo-uniform grids. This family of mixed finite element methods can be
thought of in the numerical weather prediction context as a generalisation of
the popular polygonal C-grid finite difference methods. There are a few major
advantages: the mixed finite element methods do not require an orthogonal grid,
and they allow a degree of flexibility that can be exploited to ensure an
appropriate ratio between the velocity and pressure degrees of freedom so as to
avoid spurious mode branches in the numerical dispersion relation. These
methods preserve several properties of the C-grid method when applied to linear
barotropic wave propagation, namely: a) energy conservation, b) mass
conservation, c) no spurious pressure modes, and d) steady geostrophic modes on
the -plane. We explain how these properties are preserved, and describe two
examples that can be used on pseudo-uniform grids: the recently-developed
modified RT0-Q0 element pair on quadrilaterals and the BDFM1-\pdg element pair
on triangles. All of these mixed finite element methods have an exact 2:1 ratio
of velocity degrees of freedom to pressure degrees of freedom. Finally we
illustrate the properties with some numerical examples.Comment: Revision after referee comment
Geostrophic balance preserving interpolation in mesh adaptive shallow-water ocean modelling
The accurate representation of geostrophic balance is an essential
requirement for numerical modelling of geophysical flows. Significant effort is
often put into the selection of accurate or optimal balance representation by
the discretisation of the fundamental equations. The issue of accurate balance
representation is particularly challenging when applying dynamic mesh
adaptivity, where there is potential for additional imbalance injection when
interpolating to new, optimised meshes.
In the context of shallow-water modelling, we present a new method for
preservation of geostrophic balance when applying dynamic mesh adaptivity. This
approach is based upon interpolation of the Helmholtz decomposition of the
Coriolis acceleration. We apply this in combination with a discretisation for
which states in geostrophic balance are exactly steady solutions of the
linearised equations on an f-plane; this method guarantees that a balanced and
steady flow on a donor mesh remains balanced and steady after interpolation
onto an arbitrary target mesh, to within machine precision. We further
demonstrate the utility of this interpolant for states close to geostrophic
balance, and show that it prevents pollution of the resulting solutions by
imbalanced perturbations introduced by the interpolation
On the rate of convergence of the Hamiltonian particle-mesh method
The Hamiltonian Particle-Mesh (HPM) method is a particle-in-cell method for compressible fluid flow with Hamiltonian structure. We present a numer- ical short-time study of the rate of convergence of HPM in terms of its three main governing parameters. We find that the rate of convergence is much better than the best available theoretical estimates. Our results indicate that HPM performs best when the number of particles is on the order of the number of grid cells, the HPM global smoothing kernel has fast decay in Fourier space, and the HPM local interpolation kernel is a cubic spline
Invariant higher-order variational problems II
Motivated by applications in computational anatomy, we consider a
second-order problem in the calculus of variations on object manifolds that are
acted upon by Lie groups of smooth invertible transformations. This problem
leads to solution curves known as Riemannian cubics on object manifolds that
are endowed with normal metrics. The prime examples of such object manifolds
are the symmetric spaces. We characterize the class of cubics on object
manifolds that can be lifted horizontally to cubics on the group of
transformations. Conversely, we show that certain types of non-horizontal
geodesics on the group of transformations project to cubics. Finally, we apply
second-order Lagrange--Poincar\'e reduction to the problem of Riemannian cubics
on the group of transformations. This leads to a reduced form of the equations
that reveals the obstruction for the projection of a cubic on a transformation
group to again be a cubic on its object manifold.Comment: 40 pages, 1 figure. First version -- comments welcome
Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial
Background:
In this study, we aimed to evaluate the effects of tocilizumab in adult patients admitted to hospital with COVID-19 with both hypoxia and systemic inflammation.
Methods:
This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]), is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. Those trial participants with hypoxia (oxygen saturation <92% on air or requiring oxygen therapy) and evidence of systemic inflammation (C-reactive protein ≥75 mg/L) were eligible for random assignment in a 1:1 ratio to usual standard of care alone versus usual standard of care plus tocilizumab at a dose of 400 mg–800 mg (depending on weight) given intravenously. A second dose could be given 12–24 h later if the patient's condition had not improved. The primary outcome was 28-day mortality, assessed in the intention-to-treat population. The trial is registered with ISRCTN (50189673) and ClinicalTrials.gov (NCT04381936).
Findings:
Between April 23, 2020, and Jan 24, 2021, 4116 adults of 21 550 patients enrolled into the RECOVERY trial were included in the assessment of tocilizumab, including 3385 (82%) patients receiving systemic corticosteroids. Overall, 621 (31%) of the 2022 patients allocated tocilizumab and 729 (35%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0·85; 95% CI 0·76–0·94; p=0·0028). Consistent results were seen in all prespecified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital within 28 days (57% vs 50%; rate ratio 1·22; 1·12–1·33; p<0·0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (35% vs 42%; risk ratio 0·84; 95% CI 0·77–0·92; p<0·0001).
Interpretation:
In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes. These benefits were seen regardless of the amount of respiratory support and were additional to the benefits of systemic corticosteroids.
Funding:
UK Research and Innovation (Medical Research Council) and National Institute of Health Research
Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial
Background:
Many patients with COVID-19 have been treated with plasma containing anti-SARS-CoV-2 antibodies. We aimed to evaluate the safety and efficacy of convalescent plasma therapy in patients admitted to hospital with COVID-19.
Methods:
This randomised, controlled, open-label, platform trial (Randomised Evaluation of COVID-19 Therapy [RECOVERY]) is assessing several possible treatments in patients hospitalised with COVID-19 in the UK. The trial is underway at 177 NHS hospitals from across the UK. Eligible and consenting patients were randomly assigned (1:1) to receive either usual care alone (usual care group) or usual care plus high-titre convalescent plasma (convalescent plasma group). The primary outcome was 28-day mortality, analysed on an intention-to-treat basis. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.
Findings:
Between May 28, 2020, and Jan 15, 2021, 11558 (71%) of 16287 patients enrolled in RECOVERY were eligible to receive convalescent plasma and were assigned to either the convalescent plasma group or the usual care group. There was no significant difference in 28-day mortality between the two groups: 1399 (24%) of 5795 patients in the convalescent plasma group and 1408 (24%) of 5763 patients in the usual care group died within 28 days (rate ratio 1·00, 95% CI 0·93–1·07; p=0·95). The 28-day mortality rate ratio was similar in all prespecified subgroups of patients, including in those patients without detectable SARS-CoV-2 antibodies at randomisation. Allocation to convalescent plasma had no significant effect on the proportion of patients discharged from hospital within 28 days (3832 [66%] patients in the convalescent plasma group vs 3822 [66%] patients in the usual care group; rate ratio 0·99, 95% CI 0·94–1·03; p=0·57). Among those not on invasive mechanical ventilation at randomisation, there was no significant difference in the proportion of patients meeting the composite endpoint of progression to invasive mechanical ventilation or death (1568 [29%] of 5493 patients in the convalescent plasma group vs 1568 [29%] of 5448 patients in the usual care group; rate ratio 0·99, 95% CI 0·93–1·05; p=0·79).
Interpretation:
In patients hospitalised with COVID-19, high-titre convalescent plasma did not improve survival or other prespecified clinical outcomes.
Funding:
UK Research and Innovation (Medical Research Council) and National Institute of Health Research
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