scholarly journals Expanding Grids for Efficient Cloud Dynamics Simulations Across Scales

2020 ◽  
Vol 6 (1) ◽  
pp. 38-49
Author(s):  
David H. Marsico ◽  
Samuel N. Stechmann
Keyword(s):  
Deep Convection ◽  
Computational Cost ◽  
Cost Savings ◽  
Grid Spacing ◽  
Boundary Layer Turbulence ◽  
Cloud Dynamics ◽  
Large Eddy ◽  
Shallow Clouds ◽  
Dynamics Simulations ◽  
O 10

AbstractWith large eddy simulations (LES) and/or cloud-resolving models (CRMs), it is now possible to simultaneously simulate shallow and deep convection. However, using traditional methods, the computational expense is typically very large, due to the small grid spacings needed to resolve shallow clouds. Here, the main purpose is to present a method that is computationally less expensive by a factor of roughly 10 to 50. Unlike traditional grid stretching of only the vertical z grid spacing, the present method involves expansion of the grid spacing in all coordinate directions (x,y,z) and time t. A ˝ne grid spacing of O(10)-O(100) m can be used near the surface to resolve boundary layer turbulence, and the grid spacing expands to be O(1000) m at higher altitudes, which reduces computational cost while still resolving deep convection. Example simulations are conducted with a simpli˝ed LES/CRM in 2D to verify the theoretical cost savings.

scholarly journals Numerical Accuracy of Advection Scheme Necessary for Large-Eddy Simulation of Planetary Boundary Layer Turbulence

2021 ◽  
Author(s):  
Yuta Kawai ◽  
Hirofumi Tomita
Keyword(s):  
Boundary Layer ◽  
Large Eddy Simulation ◽  
Fourth Order ◽  
Grid Spacing ◽  
Numerical Accuracy ◽  
Order Of Accuracy ◽  
Dispersion Error ◽  
Eddy Simulation ◽  
Large Eddy ◽  
O 10

AbstractRecently, large-eddy simulation (LES) has been increasingly employed in meteorological simulations because it is a promising method for turbulent parameterization. However, it is still difficult to affirm that the numerical accuracy required for a dynamical core is fully understood. In this study, we derived two theoretical criteria for the order of accuracy of the advection term in a typical situation of the atmospheric boundary layer, and demonstrate their validity by numerical experiments. In the targeted grid-spacing of O (10 m), we determined the required order of accuracy as follows: Based on the criterion of the numerical diffusion error, the upwind scheme must have at least seventh-order accuracy. The fourth-order central scheme is barely acceptable with fourth-order explicit diffusion, provided that its coefficient is one or two orders of magnitude smaller than the implicit diffusion coefficient of the third-order upwind scheme. Based on the criterion of numerical dispersion error, at minimum, the seventh or eighth order is required. The dispersion error was indirect for the energy spectra, although we expect it may affect the local turbulence mechanism. We also investigated the effects of temporal discretization for compressible models, and found that relatively lower-order time schemes are available up to the O(10 m) grid spacing if the time step is sufficiently small due to sound wave limitations. The importance of the derived criteria is that the required order of accuracy increases as the grid spacing decreases. This suggests that considerable care should be taken regarding the numerical error problem for future high-resolution LES.

scholarly journals An Anisotropic Subgrid-Scale Parameterization for Large-Eddy Simulations of Stratified Turbulence

2020 ◽  
Vol 148 (10) ◽  
pp. 4299-4311
Author(s):  
Sina Khani ◽  
Michael L. Waite
Keyword(s):  
Equations Of Motion ◽  
Computational Cost ◽  
Large Eddy Simulations ◽  
Subgrid Scale ◽  
Stratified Turbulence ◽  
Grid Spacing ◽  
Large Eddy ◽  
Vertical Grid ◽  
Ocean Models ◽  
Les Model

AbstractSubgrid-scale (SGS) parameterizations in atmosphere and ocean models are often defined independently in the horizontal and vertical directions because the grid spacing is not the same in these directions (anisotropic grids). In this paper, we introduce a new anisotropic SGS model in large-eddy simulations (LES) of stratified turbulence based on horizontal filtering of the equations of motion. Unlike the common horizontal SGS parameterizations in atmosphere and ocean models, the vertical derivatives of the horizontal SGS fluxes are included in our anisotropic SGS scheme, and therefore the horizontal and vertical SGS dissipation mechanisms are not disconnected in the newly developed model. Our model is tested with two vertical grid spacings and various horizontal resolutions, where the horizontal grid spacing is comparatively larger than that in the vertical. Our anisotropic LES model can successfully reproduce the results of direct numerical simulations, while the computational cost is significantly reduced in the LES. We suggest the new anisotropic SGS model as an alternative to current SGS parameterizations in atmosphere and ocean models, in which the schemes for horizontal and vertical scales are often decoupled. The new SGS scheme may improve the dissipative performance of atmosphere and ocean models without adding any backscatter or other energizing terms at small horizontal scales.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach

2018 ◽  
Author(s):  
Benjamin R. Jagger ◽  
Christoper T. Lee ◽  
Rommie Amaro
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Small Molecule ◽  
Brownian Dynamics ◽  
Model Simulation ◽  
Computational Cost ◽  
Lead Selection ◽  
Delta G ◽  
Dynamics Simulations

<p>The ranking of small molecule binders by their kinetic (kon and koff) and thermodynamic (delta G) properties can be a valuable metric for lead selection and optimization in a drug discovery campaign, as these quantities are often indicators of in vivo efficacy. Efficient and accurate predictions of these quantities can aid the in drug discovery effort, acting as a screening step. We have previously described a hybrid molecular dynamics, Brownian dynamics, and milestoning model, Simulation Enabled Estimation of Kinetic Rates (SEEKR), that can predict kon’s, koff’s, and G’s. Here we demonstrate the effectiveness of this approach for ranking a series of seven small molecule compounds for the model system, -cyclodextrin, based on predicted kon’s and koff’s. We compare our results using SEEKR to experimentally determined rates as well as rates calculated using long-timescale molecular dynamics simulations and show that SEEKR can effectively rank the compounds by koff and G with reduced computational cost. We also provide a discussion of convergence properties and sensitivities of calculations with SEEKR to establish “best practices” for its future use.</p>

scholarly journals Observing the Tropical Atmosphere in Moisture Space

2018 ◽  
Vol 75 (10) ◽  
pp. 3313-3330 ◽  
Author(s):  
Hauke Schulz ◽  
Bjorn Stevens
Keyword(s):  
Large Scale ◽  
Deep Convection ◽  
Circulation Pattern ◽  
Large Scale Structure ◽  
Scale Structure ◽  
Low Rank ◽  
Substantial Part ◽  
Tropical Atmosphere ◽  
Shallow Clouds ◽  
Self Aggregation

Measurements from the Barbados Cloud Observatory are analyzed to identify the processes influencing the distribution of moist static energy and the large-scale organization of tropical convection. Five years of water vapor and cloud profiles from a Raman lidar and cloud radar are composed to construct the structure of the observed atmosphere in moisture space. The large-scale structure of the atmosphere is similar to that now familiar from idealized studies of convective self-aggregation, with shallow clouds prevailing over a moist marine layer in regions of low-rank humidity, and deep convection in a nearly saturated atmosphere in regions of high-rank humidity. With supplementary reanalysis datasets the overall circulation pattern is reconstructed in moisture space, and shows evidence of a substantial lower-tropospheric component to the circulation. This shallow component of the circulation helps support the differentiation between the moist and dry columns, similar to what is found in simulations of convective self-aggregation. Radiative calculations show that clear-sky radiative differences can explain a substantial part of this circulation, with further contributions expected from cloud radiative effects. The shallow component appears to be important for maintaining the low gross moist stability of the convecting column. A positive feedback between a shallow circulation driven by differential radiative cooling and the low-level moisture gradients that help support it is hypothesized to play an important role in conditioning the atmosphere for deep convection. The analysis suggests that the radiatively driven shallow circulations identified by modeling studies as contributing to the self-aggregation of convection in radiative–convective equilibrium similarly play a role in shaping the intertropical convergence zone and, hence, the large-scale structure of the tropical atmosphere.

scholarly journals Assimilation of Lightning Data Using a Nudging Method Involving Low-Level Warming

2014 ◽  
Vol 142 (12) ◽  
pp. 4850-4871 ◽  
Author(s):  
Max R. Marchand ◽  
Henry E. Fuelberg
Keyword(s):  
Numerical Models ◽  
Deep Convection ◽  
Computational Cost ◽  
Wrf Model ◽  
Stage Iv ◽  
Simulated Precipitation ◽  
Synoptic Forcing ◽  
Total Lightning ◽  
Mu Method ◽  
Short Time

Abstract This study presents a new method for assimilating lightning data into numerical models that is suitable at convection-permitting scales. The authors utilized data from the Earth Networks Total Lightning Network at 9-km grid spacing to mimic the resolution of the Geostationary Lightning Mapper (GLM) that will be on the Geostationary Operational Environmental Satellite-R (GOES-R). The assimilation procedure utilizes the numerical Weather Research and Forecasting (WRF) Model. The method (denoted MU) warms the most unstable low levels of the atmosphere at locations where lightning was observed but deep convection was not simulated based on the absence of graupel. Simulation results are compared with those from a control simulation and a simulation employing the lightning assimilation method developed by Fierro et al. (denoted FO) that increases water vapor according to a nudging function that depends on the observed flash rate and simulated graupel mixing ratio. Results are presented for three severe storm days during 2011 and compared with hourly NCEP stage-IV precipitation observations. Compared to control simulations, both the MU and FO assimilation methods produce improved simulated precipitation fields during the assimilation period and a short time afterward based on subjective comparisons and objective statistical scores (~0.1, or 50%, improvement of equitable threat scores). The MU generally performs better at simulating isolated thunderstorms and other weakly forced deep convection, while FO performs better for the case having strong synoptic forcing. Results show that the newly developed MU method is a viable alternative to the FO method, exhibiting utility in producing thunderstorms where observed, and providing improved analyses at low computational cost.

scholarly journals Land–atmosphere interactions in the tropics

2019 ◽  
Author(s):  
Pierre Gentine ◽  
Adam Massmann ◽  
Benjamin R. Lintner ◽  
Sayed Hamed Alemohammad ◽  
Rong Fu ◽  
...  
Keyword(s):  
Land Surface ◽  
Deep Convection ◽  
Lower Troposphere ◽  
Surface Fluxes ◽  
Surface Radiation ◽  
Spatial And Temporal Scales ◽  
Wide Range ◽  
Shallow Clouds ◽  
The Tropics ◽  
The Impact

Abstract. The continental tropics play a leading role in the terrestrial water and carbon cycles. Land–atmosphere interactions are integral in the regulation of surface energy, water and carbon fluxes across multiple spatial and temporal scales over tropical continents. We review here some of the important characteristics of tropical continental climates and how land–atmosphere interactions regulate them. Along with a wide range of climates, the tropics manifest a diverse array of land–atmosphere interactions. Broadly speaking, in tropical rainforests, light and energy are typically more limiting than precipitation and water supply for photosynthesis and evapotranspiration; whereas in savanna and semi-arid regions water is the critical regulator of surface fluxes and land–atmosphere interactions. We discuss the impact of the land surface, how it affects shallow clouds and how these clouds can feedback to the surface by modulating surface radiation. Some results from recent research suggest that shallow clouds may be especially critical to land–atmosphere interactions as these regulate the energy budget and moisture transport to the lower troposphere, which in turn affects deep convection. On the other hand, the impact of land surface conditions on deep convection appear to occur over larger, non-local, scales and might be critically affected by transitional regions between the climatologically dry and wet tropics.

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