NEMOS tutorial

Example basic data sets are provided with NEMOS and are stored in the Example Data sub-folder
under C:\\Coastal Engineering Design & Analysis System\Nemos\Example Data. This tu-
torial describes how certain NEMOS programs are used in combination to analyze and display these
basic data sets (bathymetry, wave information, and shoreline data) and to develop additional data for
carrying out a comprehensive application process.

Example basic data sets include:

A01_1yrts_wav.xls - a 1 year time series of offshore waves in a MicroSoft Excel spreadsheet

A02_bath_xyz.txt - a bathymetry given in random x-y-z ASCII text format (meters, State Plane 27,
Florida east, and the datum is MSL)
A03_99shore.txt - an ASCII text file of x-y pairs of shoreline positions (meters)

Additional example files developed from the 3 basic data files are stored on your CD in the folder
ExampleNEMOS. This tutorial describes how each file was constructed, starting with grid
development, then wave transformation, wave analysis, wave statistics, spectra derivation, RCPWAVE
and STWAVE simulations and display of results, and finally a simplified discussion of GENESIS
capabilities using a simple, straight shoreline with a protruded beach.

All files in the Example Data folder begin with a letter descriptor in order to list them in Windows
in the order they were constructed. See last slide for complete file list.
Grid Generation
An accurate computational grid is at the heart of most model applications. The first step is to
acquire accurate bathymetry data for your project site. In the example below, the project site
is essentially the entire shoreline reach. Data are imported from a file using a right click of
the mouse and selecting Import Data on the menu. The Select Grid Region icon is used to
define domain boundaries. Click Point 1 as the origin; next at Point 2 with an axis
azimuth of 279.68 deg
(the number that resulted
when the mouse was
clicked); and finally at
Point 3 to complete the 2 x
grid region. The region was Site
1
so chosen because the wave
model boundary must
follow the y-axis. Once
Waves
the grid region is selected,
a right click displays the
options and Build Uniform y
Grid is used to specify grid 3
spacing and complete the
grid development. The
graphic selection tool is
inaccurate and cartographic
layout is recommended for
actual projects. Automated
tools are excellent for quick,
initial project development.
Grid refinement and Station selection
Once the grid is built, the next step is to display the model domain and perform any necessary data
editing. In the left figure, the Polygon Tool was used to edit the offshore bathymetry and shore
topography regions not captured properly by the selection tool . The Station Selection tool was
activated to place two gage stations in the model grid. If this grid were to be used for supplying wave
information to GENESIS, a large number of such stations would be created along the offshore
GENESIS boundary. This operation can be carried out by zooming in on the project area prior to
station selection. The right figure below shows a partial zoom on the project area. The colors used
for the bathymetry contours can be changed by the user. Bathymetry visuals may be improved by
using a varied number of depth contour values and different start and ending colors for the range of
depths. The final grid has 2926 50 m grid cells (77 in the longshore and 38 in the cross-shore direction).
Files created in GRIDGEN were : B_grid.grd ; B1_grid_spd.nc ; B2_grid_sta_rcp.nc ; and
B2_grid_sta_stw.nc (grid, spatial domain, and 2 station files). Station files are I/O type files and if
you are running both wave models you will need a different station file for each.

3
Zoom Station
Grid editing
& station
selection

1 2
Wave transformation
Wave data at the grid boundary are generated by using WISPH3, a simplified point-to-point trans-
formation of waves from deeper water to an arbitrary shallower water depth. Since all the models
in NEMOS communicate with NetCDF files, the first step in using WISPH3 is to prepare the wave
data for use in the NEMOS environment by constructing a NetCDF file. This is done using the
WWWL data editor.

The Excel spreadsheet is edited by replacing the alphabetic header with a numeric header, defined
in the WWWL help topic Getting Data into WWWL, and exported as an ASCII file (A1_1yrts_wav.txt).
The header in the example shown in Figure 2 in the next slide is : 2928 2 0 1 0 These
numbers indicate the data contain 2928 ASCII records, 2 - the records relate to a specific time,
0 - water levels not included, 1 - wave data included, and 0 - wind data not included. After importing
this file into WWWL and setting data characteristics via various WWWL tabs, the data are
exported using the Station pull-down menu into a NetCDF file named A2_1yrts_wwwl.nc.

WISPH3 is now invoked to transform waves from the

offshore gage to the boundary gage. Knowledge of the
shoreline azimuth is required and in this case is 189.68 x
deg (y-axis azimuth or 279.68 - 90 = 189.68). The
next step is to flag calm events from the 1-year time Shoreline
series in case these waves are used by GENESIS - to axes
save compute time. Once flagged, the time series is
filtered to produce a time series for analysis in WSAV. Boundary gage y
Results are saved in a Permutation File for use by a wave
model.
 Figure 1

Excel file

File: A01_1yrts_wav.xls

Figure 2

Header
converted
to proper
Modified format
File: A01_1yrts_wav.xls

Figure 3

Export
data to an
File: A1_1yrts_wav.txt
ASCII file
Wave transformation - contd
The left-hand figure shows the input wave file to WISPH3 (as a *.nc file) or WWWL (in *.txt form) .
The right-hand figure shows the results from WISPH3. Note the wave heights are different after trans-
formation and the directions have been converted to a system relative to the shoreline axes.

WISPH3 Input file : A2_1yrts_wwwl.nc Resulting file : C1_BND_wav_ph3.nc

The configuration file created in WISPH3 was saved as C2_BND.wp3

Note: The steps discussed so far are simply one approach. You may not use spreadsheets, but
build your ASCII files directly. Your bathymetry may be in a different format compatible
with GRIDGEN. It will take a learning experience to become familiar with all the options
available in NEMOS.
 Analysis of wave data
WWWL is used to flagged those waves that will not
influence transport. Under the Station pull-down
menu choose Waves and then Wave Transport Range.
The default threshold parameter is used but can be
adjusted depending on wave climate energy. Clicking
OK results in flags (-99) appearing in the place of
Periods to denote calm wave conditions. The file is
saved as : C3_BND_wav_crit.nc to indicate waves
limited by a criterion. There are 2928 events in the
complete leap year (every 3 hours).

Filtering

Next, the calm waves are removed by choosing Wave

Period Range from the menu and removing the flagged
Periods by selecting a range of periods that encompass
your data. The resulting file is saved as :
C4_BND_wav_crit_nocalm.nc This file contains
2601 events and will be used in WSAV to compute
a wave analysis. A print file from WISPH3 is
saved as B3_ph3.prt
 Analysis of wave data - contd
WSAV is used to analyze a set of wave conditions for usual wave statistics. In WSAV, open Wave
Component and bring in the nocalm file saved in WWWL. Use the Edit pull-down menu to first
choose Band Limits to set range bands of Height, Period, and Direction ; then Analyze to compute the
statistics.

ASSIGN : Height Period Direction

Clicking Analyze simply runs the model and produces the statistics. Use the Plot Type pull-
down menu and select Block Diagram and Number of Occurrences. Then select Occurrence v
Theta v Period to get the plot shown on the next page. Save the file as a Permutation File for use
in either RCPWAVE or SPECGEN. Permutation File for the 30-component run:
Local Polar : D0_perm.nc WSAV print file : D0_wsav.wsv
WSAV
In the sample data the total number of occurrences
add up to 2601. Periods greater than 22 sec were
filtered. There are several ways to display statistics
in WSAV, however, this block diagram gives the
best description and tells you that the selection of
bands chosen resulted in 30 cases to run with the
wave model, each case representative of the
possible periods and direction out of the 1-year
population that may cause sediment transport.

The next advisable step is to view these results in

the WWWL editor. The wave heights are assigned
a unit value to make estimation of the shoaling
coefficient intuitive. Note that the direction con-
vention is Shore_Ref 3. If these waves are to be
processed in SPECGEN for running in STWAVE,
they must be converted to a Local Polar convention
in WWWL using Station/Waves/Change Direction
Convention. The azimuth of x-axis in the wave
model grid is 279.68 deg. Results are depicted
below.

The next step is to use these results to run

RCPWAVE or SPECGEN.
Local Polar
SPECGEN
Begin by Import Permutation File under the
File pull-down menu. Fill in the desired
frequency range for displaying results. Click
OK and a display of the first event appears on
the screen. Under Edit, Select Event will
display options. Under the Options menu you
can change plot colors and style.

Save the SPECGEN file and use for running

STWAVE.

Configuration file :
F1_SPECGEN_30.sgn

SPECGEN uses the Permutation file

created by WSAV.
 STWAVE
Running STWAVE requires opening a wave
component file, specifying certain wind & water
level conditions, and clicking on the set of file
folders containing spatial domain, station, field,
print, and configuration files.

Files used in the example case were :

Configuration file : G1_STWV4.stw
Spatial Domain : B1_grid_spd.nc
Spectrum : F1_SPECGEN_30.sgn
Field : G2_STW_fld.nc
Stations : B2_grid_sta_stw.nc
Print : G3_STW.prt

Execution time for the 30-event data set, created using WSAV, WWWL, and SPECGEN, was
approximately 12 min on a 550 MHz PC. Results are displayed on the next page.
STWAVE Example Results
The results displayed on the left show contours
of wave height for 1 event using 15 contour values.
The plot has been overlaid with wave direction
vectors.

WMV Options

Once STWAVE or RCPWAVE have been

run successfully, the Wizard Eye on the
toolbar is activated and invokes the WMV
visualization code. Many display options
are available. Additional plot options are
found under the Edit / Additional Plot
Options pull-down menu. In the left figure,
the wave height contours were plotted.
Tiling capability allows display of both field
and cross-section results. Selecting and
moving the cross section in the lower tile
will animate the cross-sectional plot above.
 RCPWAVE simulation
Using either direction convention (Local
Polar or Shore_Ref_3), the model will
accept the data, recognize the convention,
Warnings do and give the results in Local Polar.
not necessarily
negate results To run the 30 events took under 30 sec on
550 MHz machine. When running
RCPWAVE, run-time warning messages
are given by the system. These messages
indicate to the user the model is having
difficulty propagating waves over certain
areas of the bathymetry. Results are shown
for the similar STWAVE event. Also dis-
played is a shore normal cross section of
wave behavior - the wave shoals then breaks.
Files for RCPWAVE include:
E1_RCP.prt , E3_RCP_fld.nc , and
E4_RCP.rcp

Cross section
GENESIS - Basic Setup & Application
The Edit pull-down menu leads you through the various options in
setting up a GENESIS simulation. The following describes construction
of a hypothetical shoreline and example structures, use of an internal
wave model, model simulation, and visualization of results.

Step 1 : Build a Configuration file - enter title, dates, and time steps,
and save the file. Then establish the proper Coordinate System.
File specification will be discussed later. Save H1_config.gen

Step 2 : Build the shoreline - clicking Shorelines/Initial reveals the

Shoreline Editor. Either enter shoreline data by
hand (Ctrl A to add rows) or import x-y pairs.
The example shoreline is in file H2_initsh.txt .
After import and setting the start time, choose
Model Reach Preparation under the Edit menu. Later
Specifying the spatial step size and reach length
results in a shoreline table ready for GENESIS.
An example Reference Shoreline is stored in file
H3_refsh.txt . It can be prepared in the same
manner as the initial shoreline.

Step 3 : Add Structures - structures can be added using the Edit menu and
entering required data (usually the method preferred for accurately
locating the structures), or they may be entered graphically by choosing
the appropriate icon on the toolbar. In the example, a detached
breakwater (Bw) and diffracting groin (DG) were constructed graphically.
GENESIS - Basic Setup & Application - Contd
Shown is the result of graphically
constructed structures and the
breakwater characteristics reached
through the Edit pull-down menu.
The characteristics were checked
and completed by specifying Breakwater Table
depths and transmission coefficient.
Before constructing the actual
structures, zoom in on their
approximate location.

Step 4 : Set Coefficients & Boundary Zoom

Conditions - For this example we use
an internal wave model and pinned
Step 5 : Complete the Configuration file
lateral boundaries and the coeffi-
by providing a wave climate and file
cients given in the figure to the right.
names for visualizing/animating the
results and printout.

The files used for these purposes are :

Waves : H4_waves.nc
Visuals : H5_animation.vis
Print : H6_print.prt
Spatial Domain : H7_spd.nc
GENESIS - Basic Setup & Application - Contd

The wave file on the right was hand generated for the first 3
days in 1999. While not realistic, it will serve as an example.
Normally, we would provide a year or more time series. The
example GENESIS simulation is for 2 years. This 3-day
time series will automatically be repeated as long as needed
by GENESIS. Thus, assume you have a representative m-month
time series for a site. All you need supply are the data for
m-months and the series will automatically repeat it. Note, the
direction convention is Shore_Ref 1 and the azimuth of the zero
wave angle is 90 deg, consistent with the example x-axis
azimuth of 180 deg. This file is saved as a NetCDF file named
H4_waves.nc

Besides naming the print file, you can specify particular dates
where the shoreline results will be detailed in the printout.

The animation time step is called the Record-

ing time step and is specified on the Config-
uration file Dialog Box.
 Visualizing GENESIS Results
After running GENESIS (Button 3), click the animation
button (# 1) to visualize the results. Button 2 will stop 1 2 3
4
the animation. The scroll list (# 4) gives each date where
the shoreline was recorded.

The figure on the right

depicts the shoreline on
20000101. You can see
the detached breakwater
causes a tombolo formation
and the groin is capturing
sand as expected. An angle
offset of 15 degrees was
specified on the Boundary
Conditions Dialog Box in
order to bias the wave
field from the north. The
Reference shoreline is in
yellow.

The Display pull-down

menu gives many more plot
options.
GENESIS Printout
If a print file is specified
it is accessed through the
View pull-down menu.

Information has been saved

at specified dates in the
simulation.

NEMOS Wrapup
This tutorial could not
possibly cover the many
options available within the
code. The user is referred
to the technical manuals
and reports given on the CD. These reports will give guidance on modeling procedures and assumptions,
specification of default coefficients, and other useful information about individual codes within NEMOS.

When using any data editor within NEMOS remember that Ctrl A will add rows while Ctrl D
will delete rows.
 WARNING
The next slide presents a complete list of files used in
various tutorial examples. If you copy any of these files to
your PC, you must change their attributes before using
them in NEMOS.
First, you must copy the files you wish to use to a folder on
your PC.
Second, use Windows Explorer to find the folder where
you stored the files; highlight (select) all of the files.
Right click the mouse to select properties: deselect the
read only attribute.
Now the files should be ready to be used by NEMOS.
 File List
Excel Spreadsheet - one year wave time series
ASCII text file of bathymetry - x, y, z random points
ASCII text file of shoreline data points - x , y pairs
ASCII text file of Excel Spreadsheet data - modified header
NetCDF file conversion of wave time series - WWWL
GRIDGEN Configuration file
GRIDGEN Spatial Domain file
GRIDGEN Station file for use in STWAVE
GRIDGEN Station file for use in RCPWAVE
WISPH3 print file
WISPH3 transformed wave file - complete year
WISPH3 Configuration file
Filtered waves in WWWL - waves critical for transport
Filtered waves in WWWL - remove calm waves
Permutation file for 30-event set - Local Polar in WSAV
WSAV print file
RCPWAVE Print file
RCPWAVE Field file
RCPWAVE Configuration file
SPECGEN Configuration file - 30 events
STWAVE Configuration file
STWAVE Field file
STWAVE Print file
GENESIS Configuration file
ASCII text file of initial shoreline (x , y) data
ASCII text file of Reference shoreline (x , y) data
NetCDF input wave file to GENESIS
GENESIS Visualization file
GENESIS Print file
GENESIS Spatial Domain file