School of Mathematics
http://hdl.handle.net/10283/245
2019-09-11T12:11:49ZISST Deca-Alanine
http://hdl.handle.net/10283/3251
ISST Deca-Alanine
This dataset contains a deca-alanine trajectory analysed in paper "Local and Global Perspectives on Diffusion Maps in the Analysis of Molecular Systems" by Trstanova et.al. 2019. The trajectory was obtained using an implementation of the Infinite Switch Simulated Tempering method (Martinsson et. al 2018) within the MIST library with GROMACS.
2019-01-29T15:35:54ZGEOMETRIC (MITgcm) diagnostic data
http://hdl.handle.net/10283/3010
GEOMETRIC (MITgcm) diagnostic data
Dataset for the article "Implementation of a geometrically and energetically constrained mesoscale eddy
parameterisation in an ocean circulation model".
2018-01-31T16:16:44Z2DChebClass
http://hdl.handle.net/10283/2647
2DChebClass
We present a Matlab implementation of a novel, efficient pseudo-spectral collocation scheme for the solution of stiff, non-local, non-linear PDEs in one and two spatial dimensions. In particular, we compute the non-local terms in real space with the help of a specialised Gauss quadrature. Due to the exponential accuracy of the quadrature and a convenient choice of collocation points near interfaces, we can use grids with a significantly lower number of nodes than most other reported methods. We have demonstrated the capabilities of our numerical methodology by applying it to (Dynamical) Density Functional Theory problems, studying equilibrium and dynamic two-dimensional test cases with single-and multispecies hard-sphere and hard-disc particles modelled with fundamental measure theory, with and without van der Waals attractive forces, in bounded and unbounded physical domains. We have shown that our results satisfy statistical mechanical sum rules. See http://www.research.ed.ac.uk/portal/files/31208790/Pseudospectral_methods_for_density_functional_theory_in_bounded_and_unbounded_domains.pdf for details.
2017-03-24T16:04:38ZWave packet dynamics in the optimal superadiabatic approximation - Data
http://hdl.handle.net/10283/2646
Wave packet dynamics in the optimal superadiabatic approximation - Data
Data and figure files for the paper
Wave packet dynamics in the optimal superadiabatic approximation
V. Betz, B. D. Goddard, and U. Manthe
The Journal of Chemical Physics 144, 224109 (2016)
doi: 10.1063/1.4953577
Open access: http://www.research.ed.ac.uk/portal/files/25669999/NaI_trans_JCP.pdf
Abstract: We explain the concept of superadiabatic representations and show how in the context of electronically
non-adiabatic transitions they lead to an explicit formula that can be used to predict
transitions at avoided crossings. Based on this formula, we present a simple method for computing
wave packet dynamics across avoided crossings. Only knowledge of the adiabatic potential energy
surfaces near the avoided crossing is required for the computation. In particular, this means that
no diabatization procedure is necessary, the adiabatic electronic energies can be computed on the
fly, and they only need to be computed to higher accuracy when an avoided crossing is detected.
We test the quality of our method on the paradigmatic example of photo-dissociation of NaI,
finding very good agreement with results of exact wave packet calculations.
The data can be recalculated and processed using the Matlab code, also available on DataShare - http://datashare.is.ed.ac.uk/handle/10283/2645
2017-03-24T10:53:42ZWave packet dynamics in the optimal superadiabatic approximation - Matlab code
http://hdl.handle.net/10283/2645
Wave packet dynamics in the optimal superadiabatic approximation - Matlab code
Matlab code for computation of transitions through avoided crossings using superadiabatic representations.
See e.g. Wave packet dynamics in the optimal superadiabatic approximation
V. Betz, B. D. Goddard, and U. Manthe
The Journal of Chemical Physics 144, 224109 (2016)
doi: 10.1063/1.4953577
Open access: http://www.research.ed.ac.uk/portal/files/25669999/NaI_trans_JCP.pdf
Abstract: We explain the concept of superadiabatic representations and show how in the context of electronically
non-adiabatic transitions they lead to an explicit formula that can be used to predict
transitions at avoided crossings. Based on this formula, we present a simple method for computing
wave packet dynamics across avoided crossings. Only knowledge of the adiabatic potential energy
surfaces near the avoided crossing is required for the computation. In particular, this means that
no diabatization procedure is necessary, the adiabatic electronic energies can be computed on the
fly, and they only need to be computed to higher accuracy when an avoided crossing is detected.
We test the quality of our method on the paradigmatic example of photo-dissociation of NaI,
finding very good agreement with results of exact wave packet calculations.
Research data associated with this code can also be found on DataShare - http://datashare.is.ed.ac.uk/handle/10283/2646
2017-03-24T10:53:31ZEmergent eddy saturation diagnostic data
http://hdl.handle.net/10283/2365
Emergent eddy saturation diagnostic data
Dataset for the article "Emergent eddy saturation from an energy constrained eddy parameterisation".
2017-02-17T11:24:10ZSUPERSEDED - Emergent eddy saturation diagnostic data
http://hdl.handle.net/10283/2104
SUPERSEDED - Emergent eddy saturation diagnostic data
Dataset for the article "Emergent eddy saturation from an energy constrained eddy parameterisation".
Superseded by: http://datashare.is.ed.ac.uk/handle/10283/2365
2016-09-15T16:05:17Zg-BAOAB source files
http://hdl.handle.net/10283/1952
g-BAOAB source files
The files included here are the code files needed to implement the geodesic integration schemes relevant to the manuscript: "Efficient molecular dynamics using geodesic integration and solvent-solute splitting" (Proceedings of the Royal Society, 2016).
2016-04-05T16:17:52ZConstrained interpolation data (modified time discretisation and extended adaptivity settings)
http://hdl.handle.net/10283/1948
Constrained interpolation data (modified time discretisation and extended adaptivity settings)
Numerical simulations of the two-dimensional lock-exchange problem, used in the study of mesh-to-mesh interpolation effects.
2016-04-01T15:42:43ZDispersion in networks
http://hdl.handle.net/10283/1925
Dispersion in networks
Ensemble of Matlab routines to calculate the time evolution of a scalar in a network following the advection-diffusion equation.
The particular case of dispersion in the Manhattan road grid is included.
Please refer to the Readme file for more details.
Note that some routines for parsing OpenStreetMap data into Matlab data may be necesary, available here:
http://uk.mathworks.com/matlabcentral/fileexchange/35819-openstreetmap-functions
2016-02-15T12:16:38ZFast methods for training Gaussian processes
http://hdl.handle.net/10283/1924
Fast methods for training Gaussian processes
This submission includes a simplified version of some code we have been developing for fast training of Gaussian processes. We also include a sample data set, which is NOAA tidal data from Woods Hole in the US, downloaded from http://tidesandcurrents.noaa.gov/ .
The code and data included here were used to produce the numerical results in the following paper:
[1] Fast methods for training Gaussian processes, C. J. Moore, A. J. K. Chua, C. P. L. Berry, and J. R. Gair (2016), submitted to RSOS.
2016-02-12T12:05:57ZScattering of inertial waves by random flows
http://hdl.handle.net/10283/1910
Scattering of inertial waves by random flows
This dataset contains a matlab code that simulates the Young and Ben Jelloul equation for inertial waves propagating in a 2D flow. Also attached is a program to generate a 2D gaussian random flow, and a routine to calculate the eigenvalues of the scattering operator (see article arxiv.org/abs/1510.00784 )
2016-02-01T15:21:48ZEddy diffusivity diagnostics data
http://hdl.handle.net/10283/936
Eddy diffusivity diagnostics data
Coarse resolution numerical ocean models must typically include a parameterisation for mesoscale turbulence. A common recipe for such parameterisations is to invoke down-gradient mixing, or diffusion, of some tracer quantity, such as potential vorticity or buoyancy. However, it is well known that eddy fluxes include large rotational components which necessarily do not lead to any mixing; eddy diffusivities diagnosed from unfiltered fluxes are thus contaminated by the presence of these rotational components.
2015-12-03T13:39:37ZConstrained interpolation data (superseded)
http://hdl.handle.net/10283/751
Constrained interpolation data (superseded)
# This data item has been replaced by the one which can be found at https://doi.org/10.7488/ds/1362. #
2015-04-29T13:00:06ZQuasi-geostrophic double gyre force function data
http://hdl.handle.net/10283/695
Quasi-geostrophic double gyre force function data
2015-01-22T17:09:36ZParallel simplex benchmarking results
http://hdl.handle.net/10283/680
Parallel simplex benchmarking results
Data used to generate results in "Parallelizing the dual revised simplex method" http://www.maths.ed.ac.uk/hall/HuHa13/, a copy of which is attached.
2014-12-23T10:57:42ZSnapshots of an N-body model of M4
http://hdl.handle.net/10283/618
Snapshots of an N-body model of M4
326 snapshots of an N-body model of the Galactic globular cluster M4. Each snapshot consists of a list of all the particles in the simulation at one time.
2014-09-04T09:28:57ZHypFun
http://hdl.handle.net/10283/607
HypFun
MATLAB code for computing the confluent and Gauss hypergeometric functions using a range of numerical methods.
2014-07-29T11:03:16ZSymmetry operators Mathematica notebook
http://hdl.handle.net/10283/541
Symmetry operators Mathematica notebook
This is a collection of files intended for verification of the results in the paper
Andersson, L, Bäckdahl, T, Blue, P, "Second order symmetry operators", (2014) arXiv:1402.6252 [gr-qc]
to appear in Class. Quantum Grav.
2014-04-17T16:23:36Z