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Messages - Jonathan S. Clough

#271
A question was asked:

QuoteWhy do my model results look different when I select to "ignore dikes" as I have no dike layer associated with my simulation?   I am using the elevation pre-processor due to a low-vertical-resolution elevation coverage.

I responded: I think I now understand the source of this difference.

We have some logic in the pre-processor that will "boost" dry lands and fresh water wetlands above the "salt boundary" if they fall below the salt boundary.  Say, for example, that you have a contour interval of 10 feet.  In your digital elevation map (DEM) you might have a lot of dry land that, according to the NED, is below that 10 foot contour.  I have found that the DEMs from the NED assign pretty much everything under the lowest contour to some fairly arbitrary low value (Jim Titus once told me how they assigned the shoreline but I can't quite remember... maybe MHHW?... anyway).  Unless the pre-processor intervenes, a whole lot of fresh marshes and dry land convert immediately. 

To solve this problem we "boost" all of those dry-land elevations below the "salt boundary" to above the "salt boundary" (or "salt elevation.")  Like wetlands we use a uniform distribution moving away from the "direction offshore" up to the elevation of the lowest contour (this is now editable as the "upper bound" in the elevation analysis screen).

Recently I had a problem when running a site with dikes.  Land behind dikes should never be "boosted" because it often falls below the salt boundary due to the seawalls surrounding it.  I tried to run a simulation with dikes removed and did not find any conversion of dry lands that I knew were well below the salt boundary.  That was because the dikes were not being included so the software assumed that these lands needed to be "boosted."

Therefore I put in this piece of logic:

   If a cell is protected by dikes OR if the dikes are not included, then do not boost the dry land elevations.  (1-8-2010)

I did not realize that this meant a site would have different results if the site has no dikes file and if the "use dikes" option is changed.

The upshot is, with the current version, please do not run the model with "dikes turned off" if you don't have a dike file to begin with.  I guess that I need to change that logic so that it knows whether a location is diked or not, even if dikes are not included so that SLAMM knows which land to boost and which land not to boost.  (Previously the software was not even loading in the dike layer as it wasn't planning on "including dikes."   So I will have to change that logic in the software.) But in the short run, leave "include dikes" on and that will give you the "correct" answer for this site.  I'll also change the code so that it reads

   If a cell is protected by dikes OR (if a dike file exists AND if the dikes are not included), then do not boost the dry land elevations.  (2-22-2010)

That line of code should prevent further confusion as you experienced though it is not perfect (as it does not discern which lands should remain "boosted" due to their non-diked status and which lands should not).

I have to say that I have become a lot more comfortable using the model when there are high-vertical-resolution elevation data available.  This whole pre-processing and "boosting" set of procedures is really trying to make the best of a bad situation.  The model assigns uniform distributions to each wetland type from their lowest estimated range to their highest.  LiDAR data have shown us that some wetlands are perched precariously above their lowest elevation (the elevation at which point they will convert to tidal flats or open water) and other wetlands are safely located high above it.  These initial-condition elevations therefore make a difference in the extent and timing of wetland-loss predictions.  When we are forced to use the pre-processor, lacking all of that information, we just assign the wetlands with elevations over their existing range.  Boosting dry lands is similar.  You need to hope you have the correct salt elevation assigned and there is not some other factor (like tide range reduction) that allows dry land to persist at a lower elevation.

Also, when running the model with LiDAR, you have a good sense of whether your MTL to NAVD88 correction is working, and your tide ranges are parameterized properly because, if not, then you have problems with your "time-zero" results or elevation analysis.  With no LiDAR data, the model just "corrects" elevations that do not match its conceptual model, so you have no such check on your input parameters...

The uncertainty of the pre-processor is something that should be firmly caveated in any discussion of model results.  "Model uncertainty for this site is quite a bit higher due to the absence of high-vertical-resolution elevation data."

I hope that this resolves your problem, thanks for being such helpful beta testers, and I'm sorry that I didn't think of this possibility when solving my other problem with what seemed like an innocuous line of logic!  Let me know if your problem persists or if you find any other strange results.

-- Jonathan
#272
The SLAMM erosion routine tries to estimate where marsh and swamp erosion will take place by estimating maximum fetch (wave-setup).  When the maximum fetch threshold has been exceeded horizontal erosion starts to occur.

Important note:  erosion of marshes and swamps occurs only at the marsh-water interface.  Beaches and tidal flats are assumed to be protective from erosion (though not inundation).

I recommend site-specific data based on shoreline changes maps or local data if possible.  Basically you should try to determine how many horizontal meters the shoreline is moving per year in the areas that it is receding due to erosion.  These rates can be defined in a spatially variable manner if data are available.  If not, you may have to rely on the nearest available data or regional averages.

I recommend that you play with these parameters as part of a sensitivity or uncertainty analysis as well.

The SLAMM erosion routine remains simple and has not been updated in the time that I have worked with the model (since 1998).  I am hopeful that future development of this portion of the model can take place soon.

There is no database of "default" erosion and accretion rates available at this time however I recommend the following resources for your region:

Benninger, L. K. andJ. P. Chanton. 1985. Fallout of 239,240Pu and natural 238U and 210Pb in sediments of the North River Marsh, North Carolina.  EOS 66:276.

Cahoon, D.R., J. W. Day, Jr., and D. J. Reed, 1999. "The influence of surface and shallow subsurface soil processes on wetland elevation: A synthesis." Current Topics in Wetland Biogeochemistry, 3, 72-88.

Reed, D.J., D.A. Bishara, D.R. Cahoon, J. Donnelly, M. Kearney, A.S. Kolker, L.L.  Leonard, R.A. Orson, and J.C. Stevenson, 2008: "Site-Specific Scenarios for Wetlands Accretion in the Mid-Atlantic Region. Section 2.1" in Background Documents Supporting Climate Change Science Program Synthesis and Assessment Product 4.1: Coastal Elevations and Sensitivity to Sea Level Rise, J.G. Titus and E.M. Strange (eds.), EPA430R07004, Washington, DC: U.S. EPA. http://www.epa.gov/climatechange/effects/downloads/section2_1.pdf

(For a wider perspective) Stevenson and Kearney, 2009, "Impacts of Global Climate Change and Sea-Level Rise on Tidal Wetlands"  in Human Impacts on Salt Marshes a Global Perspective.2009 University of California Press.





#273
I re-downloaded the executable and reinstalled.  I re-downloaded the sample data and ran a "set map attributes" and also ran a full model execution.

No error was generated.

Please re-download the sample data and ensure you're using the latest executable.

(I did discover that the large "load" button was acting somewhat strange so I fixed that behavior...  I had enabled dragging and dropping SLAMM6 files onto the interface but somehow that affected the functioning of that particular button...  I fixed that particular problem.)

If you are still having this problem please download the new source code, run the model though your Delphi interface and let me know on which line the error is occurring.  (I know that you had compiled the previous version.)  Good luck and let me know how this problem resolves.
#274
You must unzip the OpenGL source into a subdirectory as listed above.  Do not unzip to a flat folder but retain the directory structure within the zip file.

QuoteThe resulting file structure must be placed in an OPENGL directory off of the main program directory, including the FRAMEWORK folder.    

Then, make sure that the /OpenGL is part of your search path as part of the project options.  (Project Options, Directories/Conditionals, Search Path)  This should automatically be in place though with the project file that you downloaded.  

If this does not help you'll have to tell me the file name from which the errors occurred rather than simply the line numbers...

No code writing or variable declaration is required.

Good luck!  -- J
#275
Using SLAMM / Re: protection and nwi photo data options
January 11, 2010, 07:41:12 AM
OK many months later this interface glitch has been fixed and will be part of the next release of SLAMM6, which incidentally is slated for later this week or early next.  -- Jonathan
#276
Using SLAMM / Re: Command Line Option of SLAMM
December 21, 2009, 08:36:16 AM
Hi Dean:  I brought your files into SLAMM6 and ran in the command line and ran through 2025 and the GIS output looked fine in MapWindow.  This could be a function of MapWindow being less "finicky" about ASCII input rasters than ESRI products, I'm not sure... 

I didn't run thorugh 2100 because I need my processor back.  Did you see this problem in all rasters output by your version or just those at a particular date?  Can you send me one of the "corrupted" rasters?  (From e3 in particular?)
#277
Using SLAMM / Re: Command Line Option of SLAMM
December 18, 2009, 02:48:19 PM
OK, I'll check the output.  I haven't looked at ascii output from SLAMM6 recently.   OK, now I have from our last several projects and there was no problem I could see with any of the ASCII outputs that I created.  If you want to send me the input files zipped up I'll be happy to help you debug...  -- Jonathan
#278
Using SLAMM / Re: Command Line Option of SLAMM
December 18, 2009, 01:46:04 PM
Looks weird. 

Is it the command line that's producing this problem or just that version of the model? 
Does it look like this on the screen or is this just the ASCII output produced by the software?
When I've seen this type of distortion in the past there has been a mismatch in the number of columns specified and the actual number of columns in the ascii file...
#279
Model Formulation & Parameters / Re: Accretion
December 15, 2009, 12:57:57 PM
The accretion model is identical between versions if the new accretion values are left at their default values (i.e. if none of them are input.)  -- J
#280
You're welcome.  I'm thinking I should include an "include soil saturation as a process" flag in SLAMM6 so that it can be turned on and off...  -- J
#281
Using SLAMM / Vertical/Horizontal Streaks in Model Output
December 14, 2009, 07:19:27 AM
FAQ:  What are these vertical/horizontal streaks in model output:

Answer

QuoteSoil Saturation: 

Maps of SLAMM results occasionally include green linear stripes of fresh marsh moving through what was previously dry land (red).  These stripes are a result of the SLAMM soil saturation algorithm which is geographically quite simple.  The water table for each cell is estimated by moving unidirectionally in the off-shore direction and finding the nearest wetland cells.  This water table is then adjusted for the estimated increase in the fresh water table due to sea level rise.  If the estimated water table is greater than the elevation of the dry land, saturation takes place and the dry land is predicted to be converted to wetland.

Because of the unidirectional search algorithm, horizontal streaks may appear on model results as shown above.  Despite this minor loss of geographic realism on output maps, the algorithm does provide useful information about the susceptibility of dry land to water saturation due to changes in the water table.
#282
Using SLAMM / Re: Command Line Option of SLAMM
December 11, 2009, 12:57:54 PM
As you should know, SLAMM 6 is now publicly available including open-source code:

http://warrenpinnacle.com/SLAMMFORUM/index.php?topic=55.0

As of the time of its initial release the "Command Line" option hadn't been fully integrated yet into the model and it now has.  The file structure is dramatically different in SLAMM 6 and there is a new mechanism for invoking the command line option:

Save an existing SLAMM6 file as "txt" rather than the "SLAMM6" file-type.  (If you look at that file you will see hundreds of parameters, hopefully labeled in a relatively self-evident manner.)  You can load that text file and all of your parameters will be loaded into the model.  You can pass that file-name as a parameter to the executable and the file will be loaded upon startup or the simulation will be run.  To run the simulation automatically and terminate the application on completion you must change the very last line of that file to "ExecuteImmediately: True".

The command-line capability will soon be integrated into the main release of SLAMM6 but currently you must use this link to download the latest version with command-line capabilities.

http://warrenpinnacle.com/prof/SLAMM6/SLAMM6_Command_Line.zip
#283
Using SLAMM / SLAMM6
December 11, 2009, 06:35:53 AM
SLAMM6 has arrived, don't miss it in the Model Formulation Forum http://warrenpinnacle.com/SLAMMFORUM/index.php?topic=55.0

The interface is superior.  The core code that generates SLAMM5 predictions is all but unchanged.  The model has strong backward compatibility to SLAMM5.  The code is open-source.  Feel free to post new questions or thoughts about the SLAMM6 interface in this forum.
#284
Yes, we use the trend, but starting point shifted to the NWI photo date (if the starting point predates the NWI photo date we use the historic trend up until 1990)

However, this is Relative SLR so we also account for differences in the historic trend and the global historic trend (estimated at 1.5 mm/year in SLAMM 5)

So if your site had a historic trend of 3.5 mm/year over the last 100 years or so we would assume that this 2 mm/year differential is the result of local effects, probably land subsidence primarily.  We assume that this differential will remain constant and persist over the next 100 years.  Therefore, to estimate relative SLR we calculate  the eustatic trend (adjusted to 1990) but also add an additional 2 mm/year of SLR on to that trend.

-- Jonathan
#285
Regarding the year by year SLR for 1, 1.5, and 2 meters:

Here they are, (Eustatic SLR since 1990 in CM)

        ((184.4, 276.7,  368.9),    {2025, 1 meter, 1.5 meters, 2 meters}
         (409.2, 613.8,  818.4),    {2050, 1 meter, 1.5 meters, 2 meters}
         (698.1, 1047.2, 1396.3),  {2075, 1 meter, 1.5 meters, 2 meters}
         (1000,  1500, 2000.0));   {2100, 1 meter, 1.5 meters, 2 meters}

As stated in the tech. doc, these were calculated by scaling up the A1B-maximum such that the relative rate of sea level rise is the same between the A1B scenario and the 1, 1½ and 2 meter scenarios but the extent of sea level rise by the year 2100 is allowed to vary.