This SALMASO-7_readme20250609.txt file was generated on 20250609 by Kaylee Alexander ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Large Eddy Simulations of Tall Vegetated Canopies: Momentum Statistics and TKE Budget 2. Author Information Principal Investigator Contact Information Name: Marc Calaf Institution: Mechanical Engineering, University of Utah Address: 1495 E 100 S, Salt Lake City, UT 84112 Email: marc.calaf@utah.edu ORCID: 0000-0002-8570-1185 Co-investigator Contact Information Name: Giulia Salmaso Institution: Mechanical Engineering, University of Utah Address: 1495 E 100 S, Salt Lake City, UT 84112 Email: giulia.salmaso@utah.edu ORCID: 0000-0002-6193-8110 3. Date of data collection (single date, range, approximate date) 20220101 to 20250529 4. Geographic location of data collection (where was data collected?): University of Utah, Salt Lake City, UT 5. Information about funding sources that supported the collection of the data: NSF PDM 1712538 -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC BY NC - Allows others to use and share your data non-commercially and with attribution. 2. Links to publications that cite or use the data: - TK - TK 3. Links to other publicly accessible locations of the data: NA 4. Links/relationships to ancillary data sets: NA 5. Was data derived from another source? No 6. Recommended citation for the data: Salmaso, Giulia, and Marc Calaf. 2025. "Large Eddy Simulations of Tall Vegetated Canopies: Momentum Statistics and TKE Budget." The Hive: University of Utah Research Data Repository. https://doi.org/10.7278/S5d-n96s-3gkr. --------------------- DATA & FILE OVERVIEW --------------------- 1. File List & Description Each folder indicates a study case, and it contains three NetCDF files, two for momentum related variables (Data_Momentum.nc and Data_Momentum_2D.nc), and one for TKE budget related variables (Data_Momentum_4TKE.nc). Each variable of each file represents an average over 5 hours. All variables output from the LES correspond to filtered quantities and are non-dimensionalized using the friction velocity u* = 0.313m/s, or u* = 0.58 m/s in the case of Hom_eq_gaps_pfx_9mps for velocity-related fields, and by the boundary layer height zi = 1000m for length scales. Each study case corresponds to a folder containing 3 NetCDF files named Data_Momentum.nc, Data_Momentum_2D.nc, and Data_Momentum_4TKE.nc. In the folder naming convention, the string component “_9mps” indicates that the simulation is forced by a geostrophic wind speed of 9 m s⁻¹. Each folder name further corresponds to a specific canopy configuration. In particular, the component “Hom” designates homogeneous canopies, “Gaps” denotes horizontally heterogeneous canopies containing circular gaps of bare soil, and “Patches” refers to canopies characterized by circular patches of vegetation embedded within bare soil. Within the homogeneous set, the label “_Amazon” represents the densest canopy configuration, with a leaf area index (LAI) of 7.05. The “_eq_gaps” configuration (LAI = 5.36) is designed to match the equivalent global drag force of the gap-type canopies included in Deposit 4 (“Gap_4_9mps”, “Gap_8_9mps”, and “Gap_12_9mps”). Similarly, “_eq_patches” (LAI = 1.73) matches the equivalent global drag force of the patch-type canopies featured in Deposit 6 (“Patch_4_9mps”, “Patch_8_9mps”, and “Patch_12_9mps”). The additional label “_pfx” indicates simulations forced by a normalized streamwise pressure gradient. The label “_lim” (short for “limit”) denotes a canopy configuration with minimal vegetation density, representing an extreme case of sparse canopy cover. Finally, the label “_Empty” refers to a bare soil surface with no vegetation. Furthermore, when a number appears in the folder name, it indicates the diameter of the gap or patch, in meters, scaled by a factor of 100. For example, the label “Gap_4_9mps” refers to a canopy configuration containing gaps with a diameter of D = 400 m. When multiple numbers are present, the configuration includes a combination of gap diameters. For instance, “Gap_12_8_4_9mps” denotes a case with gaps of D = 1200 m, 800 m, and 400 m. Finally, in the folder name “Patch_4_h_9mps,” the label “_h_” stands for “half,” indicating that the number of vegetation patches in this configuration is reduced by half relative to the corresponding “Patch_4_9mps” simulation. A. Filename: TKE_BUDGET_AND_RAV.tar.gz a. Filename: Hom_Amazon_9mps.tar.gz b. Filename: Hom_eq_gaps_9mps.tar.gz c. Filename: Hom_eq_patches_9mps.tar.gz d. Filename: Hom_eq_gaps_pfx_9mps.tar.gz e. Filename: Hom_lim_9mps.tar.gz f. Filename: Empty_9mps.tar.gz g. Filename: Gap_4_9mps.tar.gz h. Filename: Gap_8_9mps.tar.gz i. Filename: Gap_12_9mps.tar.gz j. Filename: Gap_12_8_9mps.tar.gz k. Filename: Gap_12_8_4_9mps.tar.gz l. Filename: Patch_4_9mps.tar.gz m. Filename: Patch_8_9mps.tar.gz n. Filename: Patch_12_9mps.tar.gz o. Filename: Patch_4_h_9mps.tar.gz p. Filename: Load_NetCDF_DataFiles.py q. Filename: readNetCDF_to_matlab.m 2. File Download Instructions: To retrieve the data, download file 20250609_DownloadScript7_Salmaso.txt to your machine, open a command line terminal and run the following command: wget -I 20250609_DownloadScript7_Salmaso.txt For more information on running this command, visit https://gnuwin32.sourceforge.net/packages/wget.htm 3. Relationship between files: Each folder indicates a study case, and it contains three NetCDF files, two for momentum related variables (Data_Momentum.nc and Data_Momentum_2D.nc), and one for TKE budget related variables (Data_Momentum_4TKE.nc). Each variable of each file represents an average over 5 hours. All variables output from the LES correspond to filtered quantities and are non-dimensionalized using the friction velocity u* = 0.313m/s, or u* = 0.58 m/s in the case of Hom_eq_gaps_pfx_9mps for velocity-related fields, and by the boundary layer height zi = 1000m for length scales. Configurations are categorized into three main groups: homogeneous canopies (Hom_Amazon_9mps,Hom_eq_gaps_9mps,Hom_eq_patches_9mps,Hom_eq_gaps_pfx_9mps, Hom_lim_9mps, Empty_9mps), canopies with circular gaps of bare soil (Gap_4_9mps, Gap_8_9mpsz, Gap_12_9mps, Gap_12_8_9mps, Gap_12_8_4_9mps), and canopies with circular patches of vegetation surrounded by bare soil (Patch_4_9mps, Patch_8_9mps, Patch_12_9mps, Patch_4_h_9mps). The numbers in the gap and patch names denote, after being multiplied by a factor of 100, the diameter D of the gaps or patches in meters. For example, Gap_4_9mps has gaps with D = 400 m. All canopy configurations have the same canopy height, hc = 39 m. The homogeneous canopy configurations differ in their vertical Leaf Area Density (LAD) profiles. Hom_Amazon_9mps represents the reference Amazonian forest with a Leaf Area Index (LAI) of 7.05. The remaining homogeneous configurations—Hom_eq_gaps_9mps, Hom_eq_gaps_pfx_9mps, Hom_eq_patches_9mps, Hom_lim_9mps, and Empty_9mps—exhibit progressively reduced LAD profiles, with corresponding LAI values of 5.36, 5.36, 1.73, 0.14, and 0.0, respectively. These canopies were designed such that Hom_eq_gaps_9mps and Hom_eq_gaps_pfx_9mps exert the same global drag force as the heterogeneous Gap_4_9mps, Gap_8_9mps, and Gap_12_9mps canopies, while Hom_eq_patches_9mps matches the global drag of Patch_4_9mps, Patch_8_9mps, and Patch_12_9mps. Hom_lim_9mps serves as a limiting case with minimal vegetation, and Empty_9mps represents a bare-soil surface devoid of vegetation. All Gap-type and Patch-type canopies adopt the Amazon LAD profile (LAI = 7.05). The Gap_4_9mps, Gap_8_9mps, and Gap_12_9mps configurations contain circular gaps of bare soil randomly distributed across the domain, with diameters of 400 m, 800 m, and 1200 m, respectively, while maintaining approximately 75% vegetation cover, consistent with Hom_eq_gaps_9mps. The Gap_12_8_9mps configuration superimposes the gaps of Gap_8_9mps and Gap_12_9mps, while Gap_12_8_4_9mps combines the gaps of Gap_12_8_9mps and Gap_4_9mps. The Patch-type canopies adopt the same geometric layout as the Gap-type configurations but with the spatial distribution of vegetation and bare soil inverted. The only exception is Patch_4_h_9mps, which features half the number of vegetated patches as Patch_4_9mps, while maintaining the same patch size and overall domain. 4. Additional related data collected that was not included in the current data package: - https://doi.org/10.7278/S5d-r15r-bdqq - https://doi.org/10.7278/S5d-bg3w-c2a3 - https://doi.org/10.7278/S5d-srwd-k33d - https://doi.org/10.7278/S5d-3ve7-pm2e - https://doi.org/10.7278/S5d-44de-p0td - https://doi.org/10.7278/S5d-kd2t-86ww 5. Are there multiple versions of the dataset? No -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: The data were generated using a Large Eddy Simulation (LES) code written in Fortran. Simulations were run at the Center for High Performance Computing (CHPC) at the University of Utah. The numerical implementation follows a standard pseudospectral approach, where horizontal derivatives are computed in Fourier space, and vertical derivatives are calculated on a vertical staggered grid with a second-order finite differences scheme. The time integration follows the second-order Adam-Bashforth scheme. Lateral boundary conditions are periodic. A stress-free-lid condition is imposed on the horizontal velocity at the top boundary, whereas a non-crossing condition is assigned to the vertical velocity. At the bottom of the domain a non-slip condition is imposed for the vertical velocity, as well as the shear stress for the horizontal components. For additional details on the LES framework used please see these publications: - TK - TK 2. Methods for processing the data: Simulations were conducted using a Large-Eddy Simulation (LES) domain of size (Lx, Ly, Lz) = (2π, 2π, 1) km, where x, y, and z denote the streamwise, spanwise, and vertical directions. The computational grid consists of (Nx, Ny, Nz) = (256,256,256) points, yielding a spatial resolution of (Δx, Δy, Δz) = (24.5, 24.5, 3.9) m. An aerodynamic roughness length of z0 = 0.01 m is imposed at the surface. Time integration is performed using a fixed time step of Δt = 0.05 s for all simulations, except for Hom_eq_gaps_pfx_9mps, which employs a smaller time step of Δt = 0.02s. All simulations are spun up for 25 hours, after which flow statistics are computed over the final 5 hours, corresponding to an averaging period of 5 hours. 3. Instrument- or software-specific information needed to interpret the data: To compute the terms in the Turbulent Kinetic Energy (TKE) budget, it is first necessary to interpolate all relevant variables onto a common grid. The following two MATLAB functions serve as examples for this purpose: one performs interpolation of 3D variables from the “w” nodes (vertical velocity grid points) to the “uvp” nodes (horizontal velocity and pressure grid points), and the other performs the inverse operation, i.e., from “uvp” to “w” nodes. From “w” nodes to “uvp” nodes: function [ovar] = from_w_to_uvp(ivar) ovar = zeros(size(ivar)); s3 = size(ivar,3); ovar(:,:,1:s3-1) = 0.5*(ivar(:,:,1:s3-1) + ivar(:,:,2:s3)); ovar(:,:,s3) = ovar(:,:,s3-1); end From “uvp” nodes to “w” nodes: function [ovar] = from_uvp_to_w(ivar) ovar = zeros(size(ivar)); s3 = size(ivar,3); ovar(2:end) = 0.5*(ivar(:,:,1:s3-1) + ivar(:,:,2:s3)); end To facilitate data access, a MATLAB script readNetCDF_to_matlab.m and Phyton script Load_NetCDF_DataFiles.py are provided. These scripts load the files and organize them into arrays for subsequent analysis. 4. Standards and calibration information, if appropriate: The velocity fields are non-dimensionalized using the velocity scale u_scale​ = 0.313 m/s. To retrieve the dimensional velocity components (u, v, w), each component needs to be multiplied by this scale factor. 5. Environmental/experimental conditions: The simulations related to the present dataset investigate heterogeneity in tall vegetated canopies designed to mimic the Amazon rainforest. Simulations are forced with a geostrophic wind speed of 9 m/s, under neutral atmospheric stratification. In particular, "Hom-Amazon" represents the actual Amazon forest, with a canopy height hc = 39 m and a LAI = 7.05. The canopy height remains the same across all configurations. In contrast, the homogeneous canopies "Hom-eq-gaps", "Hom-eq-patches", and "Hom-lim" represent forests with progressively reduced LAD profiles, with corresponding LAI values of 5.36, 1.73, and 0.14, respectively. The LES domain used in this study measures (Lx, Ly, Lz) = (2 pi, 2 pi, 1) km, where (x,y,z) denote the streamwise, spanwise, and vertical directions, respectively. The numerical grid consists of (Nx, Ny, Nz) = (256,256,256) points, resulting in a spatial resolution of (Δx, Δy, Δz) = (24.5,24.5,3.9) m. An aerodynamic roughness length of z0 = 0.01 m is imposed at the surface. A time step of dt = 0.05 s is used for time integration. All simulations are spun up for 25 h, and flow statistics are computed during the last 5 h. The data presented here is sampled in the final 5 h interval. All information about how the data were generated (i.e., geometry, forcing, and other conditions) are available in the following publications: -TK -TK 6. Describe any quality-assurance procedures performed on the data: The data were generated with a computational framework that has been often tested against other simulation platforms and experimental data. 7. People involved with sample collection, processing, analysis and/or submission: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Data_Momentum.nc ----------------------------------------- Note: Each corresponding momentum file Data_Momentum.nc includes the following variables in a Python Xarray structure. Time is average over 5 hours. 1. Number of variables: 26 2. Variable List A. Name: avgU Description: mean streamwise wind speed B. Name: avgV Description: mean spanwise wind speed C. Name: avgW Description: mean vertical wind speed D. Name: avgP Description: mean dynamic modified pressure field E. Name: avgU2 Description: used to compute the Reynolds stress components F. Name: avgV2 Description: used to compute the Reynolds stress components G. Name: avgW2 Description: used to compute the Reynolds stress components H. Name: avgUV Description: used to compute the Reynolds stress components I. Name: avgUW Description: used to compute the Reynolds stress components J. Name: avgVW Description: used to compute the Reynolds stress components K. Name: avgU3 Description: correspond to the equivalent but instead of squared they are cubed L. Name: avgV3 Description: correspond to the equivalent but instead of squared they are cubed M. Name: avgW3 Description: correspond to the equivalent but instead of squared they are cubed N. Name: avgU4 Description: correspond to the equivalent but instead of squared they are to the 4th power O. Name: avgV4 Description: correspond to the equivalent but instead of squared they are to the 4th power P. Name: avgW4 Description: correspond to the equivalent but instead of squared they are to the 4th power Q. Name: avgtxx Description: represent the corresponding averaged subgrid scale (SGS) stress R. Name: avgtyy Description: represent the corresponding averaged subgrid scale (SGS) stress S. Name: avgtzz Description: represent the corresponding averaged subgrid scale (SGS) stress T. Name: avgtxy Description: represent the corresponding averaged subgrid scale (SGS) stress U. Name: avgtxz Description: represent the corresponding averaged subgrid scale (SGS) stress V. Name: avgtyz Description: represent the corresponding averaged subgrid scale (SGS) stress W. Name: avgdudz Description: represent the averaged vertical derivatives, an averaged subgrid Nusselt number, and the Cs coefficient computed in the SGS model X. Name: avgdvdz Description: represent the averaged vertical derivatives, an averaged subgrid Nusselt number, and the Cs coefficient computed in the SGS model Y. Name: avgNut Description: represent the averaged vertical derivatives, an averaged subgrid Nusselt number, and the Cs coefficient computed in the SGS model Z. Name: avgCs Description: represent the averaged vertical derivatives, an averaged subgrid Nusselt number, and the Cs coefficient computed in the SGS model 4. Missing data codes: NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Data_Momentum_2D.nc ----------------------------------------- Note: Each corresponding momentum file Data_Momentum_2D.nc includes the following variables in a Python Xarray structure. 1. Number of variables: 1 2. Variable List A. Name: Mav_ustar Description: 2D plane friction velocity at the wall 4. Missing data codes: NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Data_Momentum_4TKE.nc ----------------------------------------- Note: Each corresponding momentum file Data_Momentum.nc includes the following variables in a Python Xarray structure. Time is average over 5 hours. Since the LES grid is staggered, not all variables have been printed on the same nodes. The majority of them are output on “uvp” nodes. Some, instead, were output on “w” nodes. The latter are: 'w', 'p', 'uw', 'vw', 'ww', 'uww', 'vww', 'wvv', 'www', 'wuu', 'up', 'vp', 'wp', 'dudz', 'dvdz', 'dwdx', 'dwdy', 'dwdz', 'txz', 'tyz', 'wtxx', 'wtyy', 'wtzz', 'utxz', 'vtyz', 'wtxz','wtyz', 'dxz', 'dyz', 'fdz', 'wfdz'. 1. Number of variables: 57 2. Variable List A. Name: u Description: mean streamwise wind speed B. Name: v Description: mean spanwise wind speed C. Name: w Description: mean vertical wind speed D. Name: p Description: mean dynamic modified pressure field E. Name: uu Description: used to compute the transport by mean advection term F. Name: vv Description: used to compute the transport by mean advection term G. Name: ww Description: used to compute the transport by mean advection term H. Name: uv Description: used to compute the transport by mean advection term I. Name: uw Description: used to compute the transport by mean advection term J. Name: vw Description: used to compute the transport by mean advection term K. Name: dudx Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. L. Name: dudy Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. M. Name: dudz Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. N. Name: dvdx Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. O. Name: dvdy Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. P. Name: dvdz Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. Q. Name: dwdx Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. R. Name: dwdy Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. S. Name: dwdz Description: represent the averaged spatial derivatives along the three cartesian directions (x,y,z) for u,v and w respectively. Used to compute the shear production term. T. Name: txx Description: represent the corresponding averaged subgrid scale (SGS) stress U. Name: tyy Description: represent the corresponding averaged subgrid scale (SGS) stress V. Name: tzz Description: represent the corresponding averaged subgrid scale (SGS) stress W. Name: txy Description: represent the corresponding averaged subgrid scale (SGS) stress X. Name: txz Description: represent the corresponding averaged subgrid scale (SGS) stress Y. Name: tyz Description: represent the corresponding averaged subgrid scale (SGS) stress Z. Name: uuu Description: used to compute the resolved turbulent transport term AA. Name: uvv Description: used to compute the resolved turbulent transport term AB. Name: uww Description: used to compute the resolved turbulent transport term AC. Name: vuu Description: used to compute the resolved turbulent transport term AD. Name: vvv Description: used to compute the resolved turbulent transport term AE. Name: vww Description: used to compute the resolved turbulent transport term AF. Name: wuu Description: used to compute the resolved turbulent transport term AG. Name: wyy Description: used to compute the resolved turbulent transport term AH. Name: www Description: used to compute the resolved turbulent transport term AI. Name: utxx Description: used to compute the SGS turbulent transport term AJ. Name: utyy Description: used to compute the SGS turbulent transport term AK. Name: utzz Description: used to compute the SGS turbulent transport term AL. Name: vtxx Description: used to compute the SGS turbulent transport term AM. Name: vtyy Description: used to compute the SGS turbulent transport term AN. Name: vtzz Description: used to compute the SGS turbulent transport term AO. Name: wtxx Description: used to compute the SGS turbulent transport term AP. Name: wtyy Description: used to compute the SGS turbulent transport term AQ. Name: wtzz Description: used to compute the SGS turbulent transport term AR. Name: up Description: used to compute the pressure transport term AS. Name: vp Description: used to compute the pressure transport term AT. Name: wp Description: used to compute the pressure transport term AU. Name: dxx Description: used to compute the dissipation term AV. Name: dyy Description: used to compute the dissipation term AW. Name: dzz Description: used to compute the dissipation term AX. Name: dxy Description: used to compute the dissipation term AY. Name: dxz Description: used to compute the dissipation term AZ. Name: dyz Description: used to compute the dissipation term BA. Name: fdx Description: correspond to a component of the drag force; used to compute the canopy dissipation term BB. Name: fdy Description: correspond to a component of the drag force; used to compute the canopy dissipation term BC. Name: fdz Description: correspond to a component of the drag force; used to compute the canopy dissipation term BD. Name: ufdx Description: used to compute the canopy dissipation term. Note: to obtain the actual drag force components, the sign must be reversed. BE. Name: vfdy Description: used to compute the canopy dissipation term. Note: to obtain the actual drag force components, the sign must be reversed. BF. Name: wfdz Description: used to compute the canopy dissipation term. Note: to obtain the actual drag force components, the sign must be reversed. 4. Missing data codes: NA 5. Specialized formats of other abbreviations used: NA