NEMOS System Components &

Typical Procedures

NEMOS
Wave, Wind, & Water Level Editor
WIS Phase III Transformation
Wave Statistical Analysis and Visualization
Spectra Generation
Grid Generation
STWAVE / RCPWAVE
Wave Model Visualization
GENESIS
Tidal Current Editor
GENESIS_T
 Tutorial Outline Slide #
• List of NEMOS models & NetCDF file discussion 3-4
• Discussion of GENESIS and model input requirements 5 - 14
• Grid generation for STWAVE / GENESIS - GRIDGEN 15 - 22
• Steps in running STWAVE [use of SPECGEN] 23 – 26
• Visualizing STWAVE (or RCPWAVE) results - WMV 27 - 32
• Steps in running GENESIS 33 - 47
• Regional contour trend – usage 48–50
• Variable transmission through breakwater 51
• Use of tidal currents 52–53
• Use of GENESIS_T 54-56
• Basic steps in using NEMOS auxiliary codes 57 – 79
• Grid generation- additional discussion 57-59
• Getting data into WWWL 60-62
• Wave transformation – Offshore to Nearshore – WISPH3 63-64
• Filters in WWWL – data reduction concepts 65-66
• Wave Statistical Analysis & Visualization – WSAV 67-69
• Running RCPWAVE 70-71
• Variable boundary conditions for STWAVE 72-75
• Nested-grid capabilities in GRIDGEN & STWAVE 76-79
• Naming files & WARNING – list of folders on your CD 80-83
 List of models in NEMOS
NEMOS file structure: NetCDF Files
Numerical models may both utilize and produce
massive amounts of data during the course of a
simulation. Data editors, models, and analysis
software require the data be efficiently organized
and accessed without unnecessary overhead. To
accomplish this in NEMOS, the Network Common
Data Form (NetCDF) interface was chosen to
meet the NEMOS data requirements.
NetCDF files are binary, direct-access, self-
descriptive, and network transparent. They are
portable on all computer systems where NetCDF
libraries have been ported. Therefore, all NEMOS
files (ASCII and NetCDF) may be utilized on UNIX
and PC Workstations as well as CRAY supercomputers. Although binary in form, NetCDF files can be
converted to an ASCII representation using the ncdump filter. Similarly, properly formatted ASCII files
can be converted to NetCDF format using the ncgen filter. The ncdump and ncgen filter codes are
installed along with CEDAS. There is also an automated ncdump code included in the NetCDF
folder on your CD ROM. See the next slide. Details on using ncdump and ncgen via a DOS command
prompt are given in the Help files.
NetCDF Software – Veri-Tech provides the NCDUMP.exe code (in the NetCDF folder on
your CD – not installed) that converts NetCDF files (*.nc files) to ASCII text.

Browse for the file to convert

Output file selected by code – change

name & location if desired
Select specific variables or ALL

Choose what to export – the header

information will always be exported

Default parameters set by code – no

need to change

Click Generate to convert and Finished

to Exit code
 GENESIS Formulation
Longshore net volume change
ΔQΔt = (∂Q/∂x).ΔxΔt
Cross-shore net volume change
ΔqΔt
Total volume change
ΔV = ΔxΔy(DB + DC)

= (∂Q/∂x)ΔxΔt + qΔxΔt
Δt -> 0

y 1 Q
Reference Slide     q   0
t D B  D C   x 
 [xo,yo] STWAVE origin in Eastings /
GENESIS coordinates in STWAVE local Northings
system are: are GENESIS shoreline point coordi-
[xs,ys] nates in Eastings / Northings
x
xs = D cos θ GENESIS grid [xg,yg] GENESIS origin in its local system
ys = D sin θ xx̂ . az azimuth of STWAVE grid
[xs,ys] yŷ
θ
W

D
ψ

  RAD{az  tan 1[( xs  x0 ) /( ys  y0 )]   }

ψ
y [xo,yo]
az
Relationship between
STWAVE and GENESIS axes

Reference Slide N
 General Information
GENESIS
Basic Data Requirements
Bathymetry
Describes nearshore bathymetric irregularities that cause local
transport gradients and produce non-uniform shoreline planforms.

Wave
Characterizes
Informationthe primary environmental forcing producing
longshore sediment transport and long-term shoreline planform
change.

Shoreline position & beach

properties
Provides required calibration data, initial conditions for forecast of
shoreline change and/or project performance evaluations.
 GENESIS
File-type Concepts
Configuration
Provides basic model setup and file association information.
Spatial Domain
Defines computation domain including all relevant spatial parameters such as
structures, locations of engineering activities, etc.

Visualization/Field
Output file containing major model results over the entire computational
domain.
Station
Wave file; maybe time or integer indexed and represent offshore waves or results
from nearshore wave transformation model.
Printable output
Output file containing summary of model simulation and basic outputs.
 Wave model / GENESIS
Grid Relationships

50 0

GENESIS grid
[JUCAR example]
 Wave model / GENESIS
Grid Relationships
Nearshore Reference Line (Station
file)
Wave information are passed from
the wave model to GENESIS via the
“Station” file. GENESIS requires wave
information at cell wall 1, located DX/2
outside (left of) the GENESIS Y-axis.
The NEMOS Grid Generation code allows
automatic positioning of the GENESIS
origin and axis based on user-specification
of the wave model grid cell co-located
with GENESIS cell wall 1 and the GENESIS
X-axis. Wave model save stations are
automatically selected via user-specified
station depth and length of X-axis.
Procedures for Shoreline
Change Modeling
• Develop Offshore Wave Time Series
 Import to NEMOS
 Statistically Analyse
• Develop Input for Wave Model
 Grid generation
 Input spectra
• Configure Wave Model
 Model Settings / File associations
 Simulate
• Develop Input for GENESIS
 Configuration / Set-up
 Calibrate / Verify
 Simulate / Forecast
 Develop Input for
Wave Model
GRID GENeration, GRIDGEN
Import bathymetry data, triangulate, inspect/modify, define grid region, generate grid,
inspect/modify, save Spatial Domain file. Specify station locations, inspect/modify, sort
stations, save Station file. GRIDGEN allows
automated station selection and GENESIS grid generation – save GENESIS
Spatial Domain file.
Wave Time Series, WWWL
Import wave information, transform (WISPH3), filter, statistically analyze
(WSAV), save Permutations file, generate input spectra (SPECGEN), save
Spectrum file.
Configure Model, STWAVE
Title, wind, and water level specifications, input and output file associations,
save Configuration file. Simulate, visualize (WMV).
 Develop Input for
GENESIS
Configuration
• Simulation title, units, Start/End dates, time step,
animation time step.
• Offshore & nearshore wave, printable output, and
visualization file associations.
• Beach, sand, & transport specifications
• Boundary conditions
Spatial Domain
• Shoreline Position Information – import, coordinate
transformation, model reach preparation.
• Structures – position in grid, length, permeability,
transmission, etc.
• Engineering activities – beach fill, bypassing, etc.
 When to use GENESIS_T?

Use GENESIS_T when the simulation will involve the

development of tombolos.
GENESIS_T is formulated in the context of an explicit
solution scheme, and requires shorter simulation time
steps than would otherwise be required using GENESIS
(implicit solution scheme).

GENESIS “T” enhancements – regional contours, tidal

currents, and variable wave transmission at detached
breakwaters are implemented in GENESIS.
Construct a STWAVE model grid and a GENESIS grid
within GRIDGEN
The example chosen is a location on the coast of Spain.

JUCAR
River
Aerial Photographs of Project Site
GRID Generation using GRIDGEN – Steps for importing data
Import JUCAR bathymetry into GRIDGEN – File JUCAR_bathyxyz.txt as
Local [first open GRIDGEN and right click on screen].
1 – Select Import Data

3 – Specify
coordinate
2 - Select file
system
and type
4 – Enter metadata

7 6
Depress the two
buttons shown
5 - Raw data appears by the arrow 7
on screen – right to remove the
click and triangulate display of points
and cells of the
background
grid triangles
 Use GRIDGEN to construct STWAVE & GENESIS grids
Once the bathymetry data are imported into GRIDGEN the grid is constructed
by manually specifying the same origin coordinates, axes length, and azimuth as
shown below for the JUCAR example case.
Right click and
select Build Uniform
Grid. The grid is
constructed manually
with the STWAVE
origin at:
Xo = 739885.841
Yo = 4338149.85
Rx = 1575 m
Ry = 3675 m
Azimuth = 255

Grid origins were

determined from a
cartographic layout
of the project area
 Next, shoreline points are imported into GRIDGEN – File
JUCARshoreline19570601.XY – this is a text file
[shoreline points can be imported before or after grid construction]

Button for displaying

shoreline points

Right click – select Import

Data and choose file and type
GENESIS auto-grid generation requires you to design the wave model grid to extend landward far
enough to include the desired GENESIS origin. The Create GENESIS Grid button allows you to
click the mouse at the desired location of Cell Wall 1 in the GENESIS grid (red circle). The GENESIS
origin will lie ½ dx away. Cell Wall 1 is forced to coincide with the center of a wave model cell. Its
coordinates are computed and appear in a dialog box that requires the GENESIS dx, axis length,
contour depth where stations are to be placed, and the frequency of station placement.

First magnify the

area where the
GENESIS origin
will be selected.

Then click the

desired location
of cell wall 1 – this
brings up the
GENESIS Grid
Specifications
dialog box. The
GENESIS origin is
already computed –
enter values for dx,
Construction
X-axis length, of the GENESIS
contour depth for grid
Stations, and place-
ment frequency.
 Adjusting location of Station Points selected by GRIDGEN

Automated selection of
Station Points

Adjust by clicking on a
Station Point and dragging
it to the desired location

Final GENESIS grid and Station Points.

Adjustments can be made to any area of
the grid by releasing the Zoom and
re-magnifying the desired area.
Final grid for running STWAVE showing all station points and GENESIS grid.
Zoom in on the bathymetry display to see overlay of GENESIS grid. Export the
wave
model Spatial Domain file (JUCAR_spd.nc), Station file (JUCAR_sta.nc), and
the GENESIS Spatial Domain file (JUCAR_GEN_spd.nc).

Final grids and

Station Points

Export all necessary files

 Steps in running STWAVE
The next steps before running GENESIS are to analyze wave data
and develop appropriate spectra for running STWAVE. In the
example JUCAR case, statistical summaries for four seasons were
used to generate a representative offshore wave time series, applied
Along the entire ocean boundary, for the original project on the
Spanish coast. These data were analyzed in WSAV and a permuta-
tion file was saved and used in SPECGEN to derive spectra (saved
as file JUCAR_spec.sgn).

A total of 67 combinations of H, T, and theta were run in STWAVE

using the grid (saved as JUCAR.grd), and results were saved in a
field file. The configuration file for STWAVE is JUCAR.stw and
print file JUCAR.prt. The field and print files are not included on
your CD due to their size. The STWAVE run modifies the
Station File by supplying information to relate any wave condition
at a station to the wave time series used to force GENESIS.
NOTE: A discussion of auxiliary codes will be given later in this tutorial.
STWAVE: Configuration file
Files
Tab

Title

Wind specifications

Water level
specifications

Tidal current
specifications

Parent / Nested grid

options

Configuration Tab
SPECGEN - Preparation for running STWAVE
For the JUCAR example problem only one year of wave data were available. These
data were analyzed using WSAV to identify 67 different wave height, period, and
direction combinations that represent wave action in the project area. WSAV produces
a permutation file of wave conditions that is used by SPECGEN to derive input spectra
for STWAVE. Sufficient bins are specified to properly represent spectral conditions.

Highest
Recommended Controls Frequency Spread energy

Event 30102

Controls Direction Spread

Wave frequency increases
with distance from center
 STWAVE simulation
STWAVE requires several files – the example problem
only requires spatial domain, spectrum, field, station, and
print files. In the example JUCAR problem, the files are:
Simulate
Invoke WMV to view results
after run completion
First save the STWAVE
Configuration file and
JUCAR.stw
JUCAR_spd.nc initiate the simulation
JUCAR_spec.sgn by clicking
Input files

JUCAR_fld.nc
JUCAR_sta.nc
JUCAR.prt

Output files
Station file is both Input & Output
 Wave Model Visualization - WMV
Select event

Input files for Field and Station

Setup Wizard

Draw Station Locations

Select primary data set to be viewed
Plot Station Data
 WMV Interface Screen

Model
Indicators

Graphical
Workspace

Grid
Orientation
 WMV
Tools

Choose Move X-section X-section Zoom

Object X-section Selection De-selection Anti-zoom

Select to move a X-section – click and hold mouse on the target X-section
and move the X-section to visualize / animate behavior of wave height
 WMV – Additional Plot Overlays

Wave height contours

Bathymetry isolines
Wave direction vectors
WMV Station Plots
Depress Show Stations button
followed by Station Plot button

With Show Station

depressed, double
click and station –
select Spectra 3D
OR H, T,  time series
 Example STWAVE results for JUCAR
Shown is a magnification of the northern end of the project; given are
contours of wave height with an overlay of Station Points.
 Steps in running GENESIS
The first step is to open a new GENESIS file and import the GENESIS Spatial
Domain file that was saved in GRIDGEN. Much of the data required by
GENESIS have already been developed in GRIDGEN. You need to complete and
save the configuration file and set conditions for Structures, Bypass, Beach fills,
Sand/Beach/Transport, and Boundary Conditions. The Coordinate System geo-
reference data have already been computed and passed to GENESIS. The initial
shoreline was imported by GRIDGEN and passed to GENESIS.
Open GENESIS, click File and open
the GENESIS Spatial Domain file:
JUCAR_GEN_spd.nc for the example
case to obtain:

Initiate GENESIS
 GENESIS setup ….. Click Edit and
select each
Configuration file: supply run and file information option to input
required data
Wave series time step must be
a multiple of GENESIS time step Coordinate system geo-reference
– created in GRIDGEN and
passed to GENESIS via spatial
domain file

Set model coefficients by

Sand, Beach & Transport
Construct groin at left end of project

Structures
[JUCAR example has no Bypass or Beach fill]
GENESIS setup - import reference or background shorelines
Select Edit/Shorelines/Initial [or Reference]

The initial GENESIS shoreline was interpolated for model application and passed
to GENESIS by GRIDGEN. For the JUCAR example, a 1965 shoreline is imported
as a reference or target for calibration results. Shoreline data are imported via
File/Import X-Y pairs; next select Edit/Coordinate transformation to convert the import-
ed data into the local GENESIS coordinate system - the proper transformation coordi-
nates are already loaded. Select Edit/Model Reach preparation to prepare the target
reference shoreline.

Displayed below are

both the original
and target reference
shoreline – 8 years
later. Calibration
efforts will attempt
to reproduce the
1965 observations.

Initial shoreline

Reference shoreline
 GENESIS setup – enter boundary conditions

Regional contours were

not used in this example.
See Help file for proper use
of adjustment factors and
interpolation settings. Shown
are default settings used in
the JUCAR example.

Settings for JUCAR

example – gated with
a groin on the left and
a moving boundary on
the right
Lateral Boundary
Conditions in GENESIS
Four types of lateral boundary
conditions are permitted in GENESIS.
Depending on the selection, various
additional data are required, such as
distance to shoreline, shoreline
orientation, and shoreline
displacement.
 GENESIS simulation

• Save Configuration file

• Save GENESIS Spatial Domain file
• Simulate by clicking

GENESIS visualization
• The graphical workspace can be exported
• Additional Plan View Selections
• Color / View options
• Shoreline comparison plots
• Transport rate plots
• Animation of shoreline evolution
• View printed output
 GENESIS results at end of simulation

Last exposure
from animated
Shoreline has retreated to near the measured shoreline evolution
1965 shoreline

Shoreline comparison

Transport rate plot

 GENESIS Display and Animation Options

Animation controls
and shoreline date
pull-down list
Start / Stop

Complete control on color Zoom tool controls

representation of project elements and shoreline toggle
 Bypassing options

GENESIS
Engineering
Activities

Beach Fills
 GENESIS – Structures via graphical
Select tool specification
Breakwater editor
Diffracting groin & jetty editor
Non-diffracting groin editor
Seawall editor

Structures can also be entered directly

using the appropriate editor, e.g.,

Seawalls
 GENESIS Structure Specification
Complex structures (T-groins, L-groins, etc.) are specified via a
combination of diffracting groins and detached breakwaters.
Diffracting groins and detached breakwaters comprising complex
structures must connect at their tips. The water depth and distance
from the X-axis (model length) must be identical at the connection
of the diffracting structures.

L-groin example using a

diffracting groin and a
detached breakwater
 Detached Breakwaters
Selected graphically – using variable
transmission [requires water level file]

Variable transmission

Magnify area of interest

and select Breakwater
All data on breakwater loaded by code – button – click left end of
can be entered manually structure & then right
end to complete

Dialog box for breakwater

with constant transmission
Groins and Jetties – Diffracting & Non-diffracting

Jetty at left end

of project site –
entered manually

Constructed graphically
• Groin details loaded by
code
• Location
• Length
• Any entry can be edited Magnify area of interest
and select appropriate groin
button – click top of groin
& then drag the mouse to the
landward end and click to
complete
 1–2
2–3
3-4
Seawalls
• Constructed graphically in 3 sections
• Location & indices filled in by code
Magnify area of
interest – click
Seawall button,
and click mouse
at the leftmost 3
1 4
point in the seawall (1). 2
Drag mouse to the end
of the 1st section & click (2);
drag mouse to the end of
the 2nd section & click (3);
then drag mouse to the end
of the 3rd section (4) and double click to signify end of the structure.
GENESIS – Shoreline Editor
The initial shoreline can be entered manually, imported
via the Shoreline Editor, or passed to GENESIS in the
Spatial Domain file created in GRIDGEN. The Reference
Shoreline is automatically loaded with the same data as
the initial shoreline. New data may be imported from
a text x-y pairs file and used, for example, as a target
shoreline to match in a calibration/verification effort.

When importing new data [usually in the original

coordinate system of the data imported into GRIDGEN],
you generally must select Edit/Coordinate Transformation
to convert the data to the local coordinate system used by
GENESIS. The next step is to select Edit/Model Reach
Preparation to interpolate the random shoreline data
onto the GENESIS grid.

If the GENESIS grid was created in GRIDGEN, the code

computes and passes the x- and y-origin translation
distances to GENESIS – otherwise you must compute
these quantities – see the Help Files.
 Regional Contour Trend in GENESIS
Specification of regional, stationary offshore features for transforming
waves in the internal GENESIS wave module is used to aid determination
of the long-term equilibrium planform of highly crenulated beaches in the
absence of coastal structures. The pre-specified contour is supposed to
reflect the impact of features and processes that are otherwise not
represented in the GENESIS simulations.
13600

13200
D is tance From B a seline (m )

Sample illustration of
12800
measured shoreline
and the associated
12400
regional trend
M easured Shoreline
Regional Trend
12000

11600
36000 40000 44000 48000
D istanc e A longshore (m )
 Example of how to input a regional contour trend
In this example we use the JUCAR case [in lieu of a separate
example - realize that in the JUCAR case a regional contour
trend is not needed]. The measured 1965 shoreline itself is
used as the regional contour.
Check button:
Regional contour trend specified
Then select button bar:
Enter regional contour trend
Then click Import x-y pairs
to import the correct regional
trend shoreline – remember to do a
coordinate transformation & model
reach preparation if necessary
 Results from using ’65 shoreline as a
regional contour trend
The magenta shore-
line is the regional
contour trend –
previously this
shoreline was the
Reference shoreline
and target for cali-
bration efforts.

You can see the use

of a regional trend
will definitely
impact
results.
Example files:
JUCAR_REG.gen
JUCAR_REG_GENspd.nc
JUCAR_REG_vis.nc
JUCAR_REG.prt
 Use of Variable Transmission Breakwater in JUCAR Example
For demonstration purposes, a detached breakwater
is constructed in the JUCAR example grid. Use of Structure location & properties
variable transmission requires input of a water level loaded by code
file created within WWWL. The file in this example
is: JUCAR_tide.nc The file contains an average daily
tidal cycle used throughout the simulation.
Normally, if tidal variation were
important, one would use more
refined representations, e.g.,
a representative 28-day tidal
cycle. Simulation time steps
should be  3 hrs.

Example files:
JUCAR_BRK.gen
JUCAR_BRK_GENspd.nc Structure created graphically
JUCAR_BRK_vis.nc
JUCAR_BRK.prt

Results at end
of simulation
 Tidal Current Editor
This code imports
tidal current data
in ASCII format
and prepares it for
use in GENESIS
2 - Enter the year, month,
day, and hour (24-hr 1 – Select File/Import Data
clock) for starting time
of the tidal current data
set. Also enter the time
to get
step in minutes between
events on the input file.

The tidal editor compiles the data into 8

events, one every 3 hrs covering a 24-hr day.
Data can be edited directly and are dis-
played by selecting the event from a pull-
down list. Output: *.tdl file
 Example use of tidal currents in JUCAR case
Again, in this example we use the JUCAR case [in lieu of a separate example – realize
that in the JUCAR case tidal currents were not available nor used]. Tidal currents may
come from measurements or from an application of a hydrodynamic model. The
currents used here are fictitious but representative of a typical variation across a project
reach. In the example case a KTIDE = 1.0 – currents are low and have little impact.

No tidal currents – original example case

Tidal currents – KTIDE = 1.0

No currents Currents
 Using GENESIS_T
Recall that GENESIS_T is formulated in the context of an
explicit solution scheme, and requires shorter simulation time
steps than would otherwise be required using GENESIS
(implicit solution scheme). GENESIS_T should only be
used if there is a possibility for tombolo formation. Dialog
screens for GENESIS_T are identical to those of GENESIS.
Invoke GENESIS_T by your selection on the list of models
in NEMOS.

The JUCAR example was run using GENESIS_T, keeping

all of the data (model coefficients and boundary conditions)
the same. The figure on the right shows a
comparison of the final shorelines computed
by the two different solution schemes and
the difference plot between the two. The
GENESIS_T simulation was run with a
1-hr time step as compared with the 6-hr
time step used in the GENESIS simulation.

If you select a time step for GENESIS_T

that results in model instability, a warning
is posted on the GENESIS Model Execution
screen (see next slide).
Model Instability
The JUCAR example was run with a 200 m breakwater and a 6-hr time step. The
simulation requires
a time step of
approximately 1 hr
for stable
computation.
Here you see the
warning messages
and the obvious
deterioration
in the solution
of shoreline
position.
 Tombolo Formation June 1957
To illustrate how a detached breakwater will influence
the simulation, the JUCAR example was run with an
extended detached breakwater (approximately 500 m)
at a 5 m depth. The same example was run with a
200 m breakwater to get the sequence below:
June 1959
June 1957

June 1959
June 1964

May 1962

July 1965
July 1965

Warning – these applications are for illustrative

purposes only
 Basic Steps in using NEMOS auxiliary codes
Example key 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. The
following slides describe how certain NEMOS programs are used in combination to edit, analyze,
and display these key data sets (bathymetry, wave information, and shoreline data)
and to develop additional data for carrying out a comprehensive application process.

Example key data sets include:

A01_1yrts_wav.xls - a 1-year time series of offshore waves in a MicroSoft EXCEL spreadsheet
in Meteorological angle convention

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, State Plane 27)

Additional example files developed from the 3 key or basic data files are stored on your CD in the
folder FloridaExample. The following describes how each file was constructed, starting with grid
development, then wave transformation, wave analysis, wave statistics, and RCPWAVE usage.

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 slide xx for complete file list.
Grid Generation – Additional discussion
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
y
options and Build Uniform
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, Note: Figure displays an older version of CEDAS – new tool
N
buttons have been added but older buttons are unchanged
initial project development. o
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
Note: Figure displays an older version of CEDAS – new tool
buttons have been added but older buttons are unchanged
 Getting data into the editor - WWWL
Current WIS format
• Manual Entry Spectral-based Hmo & associated
• Specify metadata
parameters only – no components
• Import ASCII file
• Specify metadata
• Import existing NetCDF file
• Import WIS database file

Typical ASCII file

WIS primary & secondary components are
treated and processed as separate files

Pre-2004 WIS formatted includes

primary & secondary components
as well as Hmo , Tp , 
 Metadata for the waves and location tabs in WWWL

Location Waves

Direction Conventions
Transformation among
differing conventions is
STWAVE
computed within WWWL
RCPWAVE

GENESIS
SBEACH NMLong-CW WISPH3
 Data Editing outside WWWL
EXCEL files cannot be imported directly into WWWL. In this example, the original data is in EXCEL.
Wave data in 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.

Original
File: A01_1yrts_wav.xls

Modified
File: A01_1yrts_wav.xls
with Header converted to proper
WWWL format

File: A1_1yrts_wav.txt
Export data to an ASCII file for input
to WWWL and save as a NetCDF file:
A2_1yrts_wwwl.nc
 Use of wave data in NEMOS
Generally, wave data are available from offshore measurement buoys or from
a hindcast database such as the WIS (Wave Information Study) data for all
coasts of the United States. Models in NEMOS require data nearer to shore.
For wave models, data are required at the wave model boundary. For GENESIS,
data are required close to the shore usually along a shallow depth contour.
Wave transformation – offshore to nearshore

NEMOS uses a simplified point-to-point transformation of waves from deeper water to

an arbitrary shallower water depth. The WISPH3 code performs this transformation.
Knowledge of the shoreline azimuth is required - in
this case 189.68 deg (same as the azimuth of the
wave model’s y-axis azimuth or 279.68 - 90 = 189.68).
WISPH3 assumes the input wave file has the angle
convention Shore_Reference 3. The input for
WISPH3 is prepared in WWWL.

Boundary gage

y
WISPH3 Shoreline axes
 Preparing data for WISPH3
Figure 1 shows the input wave file to WISPH3 (as a *.nc or NetCDF file) created by WWWL.
Figure 2 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.

1. WISPH3 Input file : A2_1yrts_wwwl.nc 2. Resulting file : C1_BND_wav_ph3.nc

(meteorological convention) (Shore_Reference 3 convention)

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.
 Filters in WWWL

WWWL is used to flagged those waves that

will not influence transport. 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). Direction
convention is still Shore_Reference 3.
 Reduction in data to be analyzed
Wave models in NEMOS are steady-state. To represent wave climate over a long period of time
it is necessary to analyze the wave data for its statistics. Namely, what set of Heights, Periods,
and Directions can be used to represent the complete time series of interest. This analysis is
made in the routine WSAV.

Prior to running WSAV, it is necessary to eliminate the low-energy wave data flagged in the
previous slide. Again a filter is used in WWWL to remove 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 change to Local Polar is made by
opening this file in WWWL and converting.
Remember, the wave models assume the
Local Polar convention for incident waves.
A print file from WISPH3 is saved as
B3_ph3.prt
 Wave Statistical Analysis & Visualization - WSAV
WSAV is used to analyze a set of wave conditions for usual wave statistics. In WSAV, open Wave
Component and import 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.
If you have more than one wave component, they are
loaded separately. Statistics are computed for the
“total” wave.

After bands are assigned, clicking

Analyze runs the analysis program.

Assign “bands” for

H, T, and 

Period Direction

Height
Block Diagram
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 a good description and tells you
that the selection of bands chosen resulted in 29 cases to
run with a 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 review these results in the

WWWL editor. The wave heights are assigned a unit
value to make estimation of the shoaling coefficient
intuitive. If substantial breaking is expected prior to
waves reaching shore, height bands should be applied.
Note that the permutation file is indexed rather than
time related. If these wave conditions are used to drive
GENESIS, an index look-up scheme is used to assign wave
Conditions, based on the incident wave time series, at each
station point fronting the beach.

The next step is to use these results to run

RCPWAVE or SPECGEN [prior to STWAVE].
 Output from WSAV

WSAV produces a 29-component “permutation” file for use in either RCPWAVE or

SPECGEN and STWAVE. The Permutation File for the 29-component run:
Local Polar : D0_perm.nc WSAV print file : D0_wsav.wsv

The file: C1_BND_wav_ph3.nc which is in Shore_Reference 3 would be brought into WWWL

and a conversion to Local Polar [or Shore_Reference 1] made to be able to use these data as
the incident wave time series to drive GENESIS. However, there is no constraint in GENESIS and
the convention of the incident wave file will be adjusted to fit GENESIS.
Permutation file – integer
indexed
30201 – Angle band 3
Period band 2
Height band 1

Histogram
 RCPWAVE Simulation
Use permutation file D0_perm.nc
First supply title, specification of incident wave
Configuration Tab condition, and water level information.
Default model constants are suggested for all
simulations – check model theory if adjustment
is needed. Select information to be saved on
the Output Tab.

Save the configuration file and select

to begin the simulation.

Solution Tab
Model Constants
Files Tab
 RCPWAVE Messages & Results

When running RCPWAVE, run-time

Warnings do warning messages are given by the
not necessarily system. These messages indicate to
negate results the user the model is having difficulty
propagating waves over certain areas
of the bathymetry.

Results are shown for the similar

STWAVE event. Also displayed 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
Variable Ocean Boundary for STWAVE
Below is an example using the JUCAR data set. In GRIDGEN, ocean boundary stations
are created at each end of the wave model grid (only one is shown) where different wave
information is known. If the grid is to be used for driving GENESIS, the GENESIS
spatial domain and station files are exported prior to selecting the ocean boundary
stations. See the details on this procedure in STWAVE_V on your CD. Wave data
from the ocean boundary stations are processed separately in WWWL – locations
of the stations are imported on the WWWL Location tab. Use WSAV to analyze all
wave
data together, followed by running SPECGEN to create the input spectra for multiple
stations on the wave model boundary. It is important that the results of WSAV indicate
a consistent set of Hmo, Tp, and  combinations for each oceanWaves:
boundary station.
Waves_OB1.nc
Waves_OB2.nc
OB1_perm.nc
OB2_perm.nc

Ocean boundary
station example Ocean boundary
station at upper
left corner
 Consistent Categories of Hmo, Tp, and  Events
The original JUCAR waves file for this
example is renamed: Waves_1.txt
The angles were modified by 5% to
Analysis of create a similar wave file to illustrate
Waves_OB1.nc use of variable spectra on the ocean
boundary. Waves_2.txt is the modified
wave file. These files are brought into
WWWL to create Waves_OB1.nc &
OB2. WSAV is used to analyze these
files resulting in the categories shown.

Analysis of
Two permutation files are produced in Waves_OB2.nc
WSAV and imported into SPECGEN
where a single *.sgn file containing two
stations is produced.
Bands used:
H – 0 , 15
T – 2 , 4 , 6 , 8 , 12 , 15
 - 90 , 60 , 20 , -20 , -60 , -90
Run SPECGEN
Import permutation files one-by-one and derive spectra. Make sure the categories
of events are consistent – proper interpolation must be made. In the example below
two stations were
created on the
JUCAR open
boundary – the
difference being
Consistent Categories for both Stations slightly different
wave angles.

Events for Station

X = 0.0 and Y = 3675.0

Results from SPECGEN are saved as a single

*.sgn file to drive STWAVE – OB_DualSPEC.sgn
STWAVE model setup for running variable ocean boundary conditions

SPECGEN
input file with
Multiple Stations

This example is a parent grid with

variable ocean boundary conditions –
select the mode of interpolation
As an illustration, spectra at the ocean stations are computed in SPECGEN.
Spectra at all interior boundary points are interpolated in STWAVE from the
spectral data given at the corners of the ocean boundary
Nested Grids in STWAVE and GRIDGEN
To use a nested grid in STWAVE, first develop both parent and nested grid in GRDIGEN.
The example below was constructed using the JUCAR data. The parent grid is shown –
click the Nested Grid tool and generate
the nested domain in a similar manner as
constructing the parent grid. Here the
parent grid has a resolution of 25 m and
the nested grid 10 m. The nested grid
can be constructed graphically (clicking
the mouse at locations 1, 2, & 3) or
3 manually. Designated stations
adjacent to the nested-grid ocean
boundary are automatically
selected by the code. Spectra will
be saved at each of the designated
1 2
stations when the parent grid is
run. The code forces you to save
the spatial domain file for the
Designated nested grid.
stations in RED
Editing the Nested Grid
Open the nested-grid spatial domain file in GRIDGEN and operate on it as you
would the parent grid. Create new stations (shown here) and / or develop a
GENESIS grid. Export the appropriate files.

Export the
appropriate
files
Running a Nested Grid in STWAVE – Parent grid results
First run the parent grid in STWAVE.
For this example a two-event
SPECGEN file was created:
Parent_spec_in.sgn
Results for both events are shown:

Output spectrum file produced by parent run:

Par_to_nest_spec.sgn
 Nested Grid results
Supply the appropriate STWAVE files for
the nested grid run. Results from both
events are shown below:

Output from parent is

now the input spectrum

Linear interpolation selected

 File Naming Conventions
Each component of NEMOS requires certain file standards to allow communication among the various codes. Below
is a listing of files names used in NEMOS and a suggested "naming" practice. A typical NEMOS session will result in
many files and it helps greatly to develop a practice of naming files such that their content can be easily recognized by
their name. File Type Suffix Designation & Typical Name
NetCDF name.nc (see HELP Topic NEMOS: NetCDF Files)
Data ASCII XYZ name_xyz.txt
ASCII XYD name_xyd.txt
Database NOS-WIS files - not implemented
Shoreline name_shl.txt
Models GENESIS Configuration name_cfg.gen
STWAVE Configuration name_cfg.stw
RCPWAVE Configuration name_cfg.rcp
Grid Generator name.grd
Incident wave name_inwave.nc
Incident Directional Spectrum name.sgn (type .nc)
Wind file name_wind.nc (produced in WWWL)
Water Level name_watL.nc (produced in WWWL)
Spatial Domain name_spd.nc
Station name_sta.nc
Field name_fld.nc
Permutations name_perm.nc
Print name.prt (text file)
Tidal Currents name.tdl

In choosing the "name" for each file, pick a name that will indicate the file's content, e.g., 1yr_ts_nocalm_inwav.nc"
might be a NetCDF file containing incident wave data from a 1-year time series where calm wave conditions have
been omitted.
 WARNING
• There are folders on your CD containing data files used or
produced by the 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.
 Folders / files on your CD pertaining to the NEMOS tutorial

FloridaExample JUCAR_CAL

JUCAR_REG

JUCAR_BRK
Folders / files on your CD pertaining to the NEMOS tutorial – cont’d
JUCAR_TIDE
Parent_Nest

JUCAR_OceanBndry

The 3 files with FULL as part of their

name were developed to save additional
output with which to demonstrate WMV
Station Plots.