EFDC_Explorer8.3 and EFDC+ Guidance New Features and Functionality Release: EFDCPlus_OMP_170914 EE8.3 Rel 170913 September 2017
Table of Contents 1 New Features of EE8.3 and EFDC+... 3 2 SEDZLJ Toxics Sub-Model... 4 2.1 Updates to SNL EFDC Code... 4 2.2 SEDZLJ Toxics Linkage... 5 3 Sigma-Zed Sub-Model Enhancements... 6 3.1 One Layer Option for the Sigma Zed Sub-model... 6 3.2 Updates to Layer Outputs... 6 3.3 Sigma-Zed Layer Resetting... 6 4 Other Updates... 8 4.1 Vertical Profile Display Options... 8 4.2 SWAN External Wave Model Updates... 9 4.3 Toxics Options Display... 11 4.4 Smooth Open Boundary Conditions Tool... 14 4.5 RPEM Initial Conditions Setting... 15 4.6 Sigma-Zed Run with Minimum One Layer... 16 4.7 Continuation Runs... 16 4.8 Jet Plume Interface Updates... 16 4.9 Dynamic Time Stepping Enhancements... 16 www.eemodelingsystem.com 2 September 2017
1 New Features of EE8.3 and EFDC+ Dynamic Solutions International, LLC continues to develop new functions and capabilities of the EFDC_Explorer Modeling System. This latest release of EE includes further enhancements focused on the Sandia National Laboratories (SNL) modifications to the EFDC code for the SEDZLJ Sedflume sediment transport model. Several minor bug fixes and tweaks have been addressed. New major features of EE8.3 and EFDC+ include the following: Mass balance conserved in SEDZLJ sediment sub-model Toxics capability added to the SEDZLJ sediment sub-model Sigma-Zed sub-model enhanced to support one vertical layer Sigma-Zed sub-model linkage files to exclude unused vertical layers Improvements to the Ice Model Minor Modifications and Bug Fixes Rooted Plant and Epiphyte sub-model initialization Continuation runs updated for enhanced Sigma-Zed and SEDZLJ models Saved plots feature updated Added new boundary condition options for SWAN Input Settings Extract vertical profiles of water column data in the format needed by EE for using profiles for setting IC s. Vertical Profile display option Tool for smooth open boundary conditions Jet plume interface updates Updates to GUI for toxics and new option to set initial conditions for DOC and POC. Added growth factor for Dynamic Time Stepping Can set bottom layer for SGZ in ViewPlan edit at bottom of form. Reset uniform layers function for Sigma-Zed www.eemodelingsystem.com 3 September 2017
2 SEDZLJ Toxics Sub-Model Up until this release, DSI s support for the SNL SEDZLJ was to simply reproduce the SEDZLJ results that the EFDC_SNL version produced. However, with EE8.3, we are now committing to ensuring proper performance, including mass balance, for sediments and toxics when using the SEDZLJ model. To that end, we have made many changes to EFDC+ to obtain valid model results for sediments and toxics when SEDZLJ is used. 2.1 Updates to SNL EFDC Code This updated EFDC+ code makes two significant revisions to the SNL EFDC code, one fixes an issue with the bed morphology adjustment and the other to lower the water depth cutoff for the bed shear calculations. The original SNL code produced significant mass balance error of 0.6% of mass loss in a three hour run when using bedload. Without bedload, the mass balance error was even larger. DSI has made improvements to the SEDZLJ sub-model, including code speed-ups as well as working on the bedload mass balance issue. We have been able to improve mass balance by a factor of 10 to 0.055% for EE8.3. It is expected this will continue to be improved in future releases. For the case without bedload being simulated, EE8.3 run now has a mass balance error of only 0.00014%. The mass balance tool is now more robust and reports more accurately with more options. The tool is accessed from Model Analysis Miscellaneous Mass Balance Tool button and is shown in Figure 1. Figure 1 EFDC Mass Balance tool. www.eemodelingsystem.com 4 September 2017
2.2 SEDZLJ Toxics Linkage Additionally, DSI have made changes so toxics are now properly handled with using SEDZLJ sub-model. This includes mass balance in the water column and sediment bed, proper working of the diffusion parameter and other improvements. While making these updates several bugs were found in the conventional EFDC toxics routines, including not maintaining mass balance, and incorrectly multiplying by bed thickness. These issues have now been corrected. The user interface for toxics when using the SEDZLJ model is the same as for the original EFDC toxics model. www.eemodelingsystem.com 5 September 2017
3 Sigma-Zed Sub-Model Enhancements A number of enhancement have been made to the Sigma-Zed model and EE as outlined below. 3.1 One Layer Option for the Sigma Zed Sub-model The Sigma-Zed sub-model has been modified to allow parts of the model domain to be reduced to one vertical layer. Previously Sigma-Zed required a minimum of two layers for all model simulations. Being able have one vertical layer is useful in situations when there are 1-D rivers feeding into a many layered reservoir or lake. Figure 2 Sigma-Zed Layer Options setting form. 3.2 Updates to Layer Outputs EFDC+ has been modified to only write out active vertical layers to the linkage files, thereby reducing the output file size significantly. In the past, the inactive layers were also written out which could lead to large file sizes. In EEMS8.3 layers below the KSZ (L) are not written to the output files because they are always zero. This approach is time invariant and is specific to SGZ model run. EE has also been updated to read the new file format, as well as continuing to load the legacy file formats. 3.3 Sigma-Zed Layer Resetting When using EFDC+ model with Sigma-Zed the user should be aware that changing the number of cells will impact the QSER.INP file. When number of cell is changed will recalculate all the layers for flow and constituents. If this is not done carefully it can lead to large file sizes as outlined below. EFDC+ supports two kinds of QSER.INP files as set in the header file. If the flag for the input type (InType.EQ.1) is 1 then EE uses layer splits. This means it will read the depth weighting for each layer and then a single value for the flow series. However, if the flag is 0 then the time stamp and flow series will be read for each individual layer. This second option can lead to large files, sometimes many gigabytes. In many case the user will have built their project and then need make a change to the bathymetry. For example, a model initially has 4 cells vertically, a change to the bathymetry by the user removes one cell from the bottom and so model requires an update to the number of cells vertically. EE will automatically reset the layering for the Sigma-Zed sub- www.eemodelingsystem.com 6 September 2017
model. EE will move all the layers so that the one bottom cell is no longer activated and the others are moved up into the top 3 cells. However, EE will see this as a user defined layer split and rebuild the QSER.INP file. This will increase the file size each time performed and the file size can get very large. Previously there was no way in EE to correct or reset the layer splits. A new option has been added to the Boundary Condition Definitions form which is accessed by Domain Boundary Conditions Edit/Review button. The user should RMC on the boundary condition to be reset and then select the Set Uniform Layer Flows as shown in Figure 3. This will total and then recalculate the layer split so that it is uniform by layer. This will reduce space and allow the model to load more quickly for Sigma-Zed models. Figure 3 Boundary Conditions: Set Uniform Layer Flows option. www.eemodelingsystem.com 7 September 2017
4 Other Updates 4.1 Vertical Profile Display Options In order to make exporting of the Vertical Profile Plots for presentations more flexible and consistent for users EE has been updated so that the user can configure how many plots are displayed on each page. So instead of 8 plots (4 x 2) as was the previous fixed layout, the user may now select 4 plots (4 x 1) or 6 plots (3 x 2) etc. This option is available by selecting the Modify Settings button in the Vertical Profile tool as shown in Figure 4. Figure 4 Vertical Profile plots display options. www.eemodelingsystem.com 8 September 2017
4.2 SWAN External Wave Model Updates Two updates have been made to the External Wave Model. The first update is the new button SWAN Input Settings has been added to the Waves SWAN Linkage which is shown in Figure 5 and serves the same function as the export SWAN settings available from ViewPlan Export Data button Export SWAN option. This facilitates the generation of the SWAN linkage files. The other update is to facilitate the offshore boundary conditions for SWAN as shown in Figure 6. Beside the local wind-generated waves which computed in the model domain by providing wind data for each model grid cells and turning on wind growth in SWAN, now the user can be able to take into account the influences of external waves (i.e., swells) acting on the model domain. EE detects the open boundary locations and let the user to edit each boundary condition for SWAN model. There are three options for each boundary condition group: No Wave, i.e. no external wave actions are taken into account at the selected boundary group. Constant: constant wave parameters in time including waves wave height, wave period, wave direction, and directional spreading are provided for the selected boundary group. Varying Time: wave parameters for the selected boundary group are varying in time and are provided in files for at least two points lying on the boundary section. The distance indicates the location along the boundary of the data point with respect to from the first grid cell (I1,J1) of the boundary group. The total length of the boundary is provided in the text box Length (m). The data file format is TPAR file described in SWAN User s Manual. Wave parameters at every grid along the boundary group will be interpolated by SWAN based on the given data files. Figure 5 SWAN linkage settings. www.eemodelingsystem.com 9 September 2017
Figure 6 Generate SWAN Model input files form. Figure 7 SWAN Boundary Conditions form. www.eemodelingsystem.com 10 September 2017
4.3 Toxics Options Display A number of updates have been made to the Toxics GUI to accommodate new features. In the main form for Toxics Toxics Options, EE now displays the average values of initial conditions for toxics in the water column as well as in the bed as shown in Figure 8. Previously the form only displayed average initial conditions of the water column for the toxic class selected in Toxics dropdown menu. This mean it wasn t clear to the user what this value was. The user can now assign the IC values directly from this form using the Assign button, or they can select the Modify button and assign them from the Initial Conditions Options tab as shown in Figure 9. Figure 8 Toxics tab: Initial conditions. www.eemodelingsystem.com 11 September 2017
Figure 9 Toxics and Sediment Bed Properties form: IC Options. www.eemodelingsystem.com 12 September 2017
Although EFDC supports the option of assigning a spatial variation for DOC and POC, up until now the EE interface didn t allow the user to set the initial conditions. In EEMS8.3 the option of setting spatial variation for DOC with the Assign button is now provided for as shown in Figure 10. Figure 10 Toxics and Sediment Bed Properties form: DOC and POC Assignments. www.eemodelingsystem.com 13 September 2017
4.4 Smooth Open Boundary Conditions Tool A common source of instability in model with open boundary conditions is caused by uneven bathymetry at the open boundaries. Rapidly changing bottom elevation at the open boundary can lead to EFDC becoming unstable. To easily resolve this issue it is recommended that the first two cells going out in the direction of the open boundary i.e. in southward direction for the southern open boundary, be at the same elevation. To facilitate this a new tool has been added to the Open Boundary Condition form as shown in Figure 11. Selecting this button will set all the first two cells the same bottom. This feature works on a group basis and uses the type ie the direction N, S, E, W, to know which cells need to be smoothed. Figure 11 Flatten Two Adjacent Interior cells button. www.eemodelingsystem.com 14 September 2017
4.5 RPEM Initial Conditions Setting Setting the initial conditions in the RPEM sub-model is now much simpler in EE. EFDC can support two kinds of IC input files. One has a header line and the other doesn t have a header line. Originally the RPEM sub-model used the sediment diagenesis value for the RPEM growth. However, if the user was not simulation sediment diagenesis then these values were zero and there was no plant growth. Therefore, a new option has been added to allows the user to set the bed porewater concentrations of ammonia, nitrate and phosphate. Another update to this is the previously EE did not do quality assurance of the data for all of the fractions for handling plant decay. Because of this in some cases the fractions did not add to one, and some splits were being lost. Now EE checks that the values are properly initialized and values add to one. Figure 12 RPEM sub-model: Set bed porewater concentrations. www.eemodelingsystem.com 15 September 2017
4.6 Sigma-Zed Run with Minimum One Layer The Sigma-Zed option in EFDC+ now runs with a minimum of one layer. Previously the minimum number of layers for SGZ was two. SGZ is now the recommended approach for modeling and is user for internal DSI models. 4.7 Continuation Runs Several updates to the Continuation Run feature have been made. Continuation runs have been updated to handle the enhancements to EFDC+ Sigma-Zed and SEDZLJ sub-models. An also issue that arose was when the last snap show of the run is equal to the last value in the restart file. This would cause the continuation option to fail. In EFDC when using a very small time-step with dynamic time stepping then it was possible that the value would be too large for EFDC to handle and lead to it crashing. 4.8 Jet Plume Interface Updates The setting for the jet plume discharge cell is not dependent on the K value. It is only dependent on the "Elevation" set for the port. The K box for the cell is now greyed out. 4.9 Dynamic Time Stepping Enhancements A new growth factor has been added to the Dynamic Time Stepping feature. This feature set the time-steps so that the delta t won t be increased for a specified number of time-steps. For example, if the current delta T is 1 second, then the new time step could be 3 seconds. With the previous options is would increase by the minimum time step. The new option will hold the time step for it jump to the maximum delta T. This makes the model more stable. Previously you could get a very high delta T, but it might become so high that the model is unstable. The new option allows the model to stay at the maximum stable time step and not go higher. Generally, it is recommended to set to about 25 for steady growth. www.eemodelingsystem.com 16 September 2017