Task 5 Report
Project:
Development of a Hydrodynamic/Salinity Model for Naples Bay and Rookery Bay
Deliverable:
Final Report
Due date:
February 14, 2014
Submitted by
Y. Peter Sheng (pete@coastal.ufl.edu), Vladimir Paramygin (pva@coastal.ufl.edu)
Contents
Data Assessment ................................................................................................................................................. 2
CH3D Model Setup .............................................................................................................................................. 8
Wind forcing .................................................................................................................................................. 11
Open boundary condition (tides) .................................................................................................................. 11
River boundary conditions ............................................................................................................................ 13
Salinity boundary conditions ......................................................................................................................... 13
CH3D Model Simulation Results........................................................................................................................ 13
Discussion and Recommendations for Future Work......................................................................................... 17
CH3D Model Input Files..................................................................................................................................... 18
Figure 1. Map of the domain, CH3D model grid and data stations .................................................................... 4
Figure 2. Measured water level at NOAA station 8725110 (Naples, FL) ............................................................. 5
Figure 3. Measured wind speed at NOAA station 8725110 (Naples, FL) ............................................................ 6
Figure 4. Rainfall at five DBHYDRO stations: BCBN, COLGOV, COLLISEM, MARCO and ROOK ........................... 6
Figure 5. Flow at three DBHYDRO stations: GG1, GG2 and HC1 ......................................................................... 7
Figure 6. Stage at seven DBHYDRO stations: GG1, GG2, GOLDW1, GRDN, HALDEMAN, HC1 and LELY41 ........ 7
Figure 7. Salinity at four Rookery Bay NERR stations: FB, FU, LH and MB .......................................................... 8
Figure 8. Salinity at three USGS stations: 02291310, 02291315, 02291330 ....................................................... 8
Figure 9. Grid Mesh. Naples Bay Area ............................................................................................................... 10
Figure 10. Measured and simulated water level at NOAA station at Naples, FL .............................................. 14
Figure 11. Measured and simulated water level at USGS station 02291310 (Gordon River) ........................... 15
Figure 12. Measured and simulated salinity at USGS station 02291310 (Gordon River) ................................. 15
Figure 13. Measured and simulated salinity at USGS station 02291310 (Gordon River), zoom-in. ................. 16
Data Assessment
Based on a review of available data, we selected a model verification time period: January through June of
2012 (six months). Figure 1 and Table 1 show locations of data stations and types of data and some details
about available data, which includes water level, flow and salinity data. Additionally, Taylor Engineering and
Interflow Engineering provided 11 data points (Figure 1) and average annual flows (Table 2) at each point that
can be used as boundary conditions.
Since the hydrologic modeling effort is still ongoing, time varying flow data are not available at the 11 stations.
Therefore, for our present project, we plan to add as many hydrological data stations (with the annual
averaged flow rates) as feasible into the Naples Bay and Rookery Bay model being developed. If the
hydrological modeling study is completed sufficiently early before the end of the current project, we will
include the time varying hydrological data into the CH3D model. Otherwise, we can include those data in
Phase II of the project.
Figures 2 through 8 show the data that were collected from different sources at the stations displayed on the
map in Figure 1.
Table 1. Summary of data available for use in the Naples/Rookery Bay model or for model verification
Station
Location
Name
USGS
02291310
Gordon
26°08'57.9"N
River
at
81°47'09.98"W
Rowing Club
Point Near
Naples, FL
USGS
02291315
Naples Bay 26°07'57.96"N
at City Dock 81°47'34.19"W
Near Naples,
FL
USGS
02291330
Naples Bay 26°05'35.28"N
at Gordon 81°47'53.31"W
Pass Near
Naples, FL
8725110
Naples, FL
26°7.9'N
81°48.4'W
RBNERR UL
Lower
Henderson
Creek, FL
26.02'57N
81.73'32W
Data Type
Frequency
Start Data
End
Data
Data
Source
Gage height [NAVD88],
salinity, temperature
15 min
Jul. 9th.
2011
Now
USGS
Gage height [NAVD88],
salinity, temperature
15 min
May. 28th.
2011
Now
USGS
Gage height [NAVD88],
salinity, temperature
15 min
May. 20th.
2011
Now
USGS
6 min /
hourly
6 min /
hourly
Dec. 21th.
1992
Jan. 1st.
1996
Now
NOAA
Now
NOAA
15 min
2001
Now
CDMO
Wind
Water level
Water
temperature,
salinity, depth
Station
Name
RBNERR UH
Upper
Henderson
Creek
RBNERR MB
Middle
Blackwater
River
RBNERR FU
Faka Union
Bay
RBNERR FB
Fakahatchee
Bay
Location
Data Type
Frequency
Start Data
End
Data
Data
Source
barometric
pressure,
wind
speed
and
direction
15 min
Jan.2004
Now
CDMO
25° 56' 3.48 N Water
temperature,
81° 35' 40.56 W salinity, depth
15 min
Jan. 2002
Now
CDMO
25° 54' 1.80 N Water
temperature,
81° 30' 57.24 W salinity, depth
15 min
Jan. 2002
Now
CDMO
25° 53' 31.92 N Water
temperature,
81° 28' 37.20 W salinity, depth
15 min
Jan. 2002
Now
CDMO
26°03.004'N
81°42.103'W
Brkpt*
Jul. 2004
Now DBHYDRO
26°10'05.017''N Water level
81°46'27.71''W Flow (daily averaged)
Daily
Sep. 2008
Now DBHYDRO
26°10'07.161''N
Water level
Brkpt*
Dec. 2008
Now DBHYDRO
81°44'03.607''W
GG2
26°10'06.406''N
Flow (daily averaged)
Daily
Dec. 2008
Now DBHYDRO
81°44'05.249''W
Brkpt*
1982
Now DBHYDRO
26°03'31.342''N Water Level
HC1
81°41'20.295''W Flow (daily averaged)
Daily
May. 2001
Now DBHYDRO
26°13'31.318''N
BCBN
Rainfall
Brkpt*
1990
Now DBHYDRO
81°48'29.304''W
26°07'47.332N''
COLGOV
Rainfall
Brkpt*
May. 1996
Now DBHYDRO
81°45'45.301W''
25°59'26.35''N
COLLISEM
Rainfall
Brkpt*
Jan. 1991
Now DBHYDRO
81°35'29.288''W
25°55'52.998''N
MARCO
Rainfall
Brkpt*
May. 2003
Now DBHYDRO
81°42'43.121''W
26°03'00.939''N
ROOK
Rainfall
Brkpt*
May. 2003
Now DBHYDRO
81°42'01.653''W
26°10'53.324''N
Oct.
NAPLE
Water level
Brkpt*
Jan. 1991
DBHYDRO
81°46'00.301''W
1999
26°10'26.326''N
GRDN
Water level
Brkpt*
Sep. 2013
Now DBHYDRO
81°47'01.302''W
26°10'04.683''N
Nov.
GOLD.W1
Water level
Brkpt*
Oct. 1964
DBHYDRO
81°46'01.848''W
2012
26°07'26.333''N
HALDEMAN
Water level
Brkpt*
Jun. 1981
Now DBHYDRO
81°45'43.301''W
26°06'14.335''N
LELY41
Water level
Brkpt*
Mar. 1980
Now DBHYDRO
81°44'46.3W''
Note: The term breakpoint is derived from the data reduction used to minimize the number of redundant
points stored in the database. Time interval may be 5-15 minutes according to the data.
GG1
Figure 1. Map of the domain, CH3D model grid and data stations
Table 2. Estimated hydrological flows
Flow Points Ranked by
Flow Magnitude
Avg. Annual Flow
(cfs)
8
6
1
9
10
3
2
7
5
4
18.49
15.97
10.48
7.66
5.23
5.18
3.69
1.42
1.12
0.69
-0.5
0
0.5
Measured
-1
Water level, m (NAVD88)
Naples, FL (8725110)
2012-01-12
2012-03-12
Figure 2. Measured water level at NOAA station 8725110 (Naples, FL)
2012-05-11
Naples, FL (8725110)
10
5
0
Wind speed, m/s
15
WindSpeed
2012-01-12
2012-03-12
2012-05-11
Figure 3. Measured wind speed at NOAA station 8725110 (Naples, FL)
3.0
2.5
2.0
1.5
0.0
0.5
1.0
Rainfall, inches
3.5
4.0
BCBN
COLGOV
COLLISEM
MARCO
ROOK
2012-01-12
2012-03-12
2012-05-11
Figure 4. Rainfall at five DBHYDRO stations: BCBN, COLGOV, COLLISEM, MARCO and ROOK
GG1
GG2
HC1
10
Flow, cfs
8
6
4
2
0
2012-01-12
2012-02-11
2012-03-12
2012-04-11
2012-05-11
2012-06-10
Figure 5. Flow at three DBHYDRO stations: GG1, GG2 and HC1
GG1
GG2
GOLDW1
GRDN
HALDEMAN
HC1
LELY41
Water level, ft (NGVD29)
8
6
4
2
0
2012-01-12
2012-03-12
2012-05-11
Figure 6. Stage at seven DBHYDRO stations: GG1, GG2, GOLDW1, GRDN, HALDEMAN, HC1 and LELY41
40
Salinity, ppt
35
30
25
20
FB
FU
LH
MB
15
10
2012-01-12
2012-02-11
2012-03-12
2012-04-11
2012-05-11
2012-06-10
Figure 7. Salinity at four Rookery Bay NERR stations: FB, FU, LH and MB
40
35
Salinity, ppt
30
25
20
15
02291310
02291315
02291330
10
5
2012-01-12
2012-02-11
2012-03-12
2012-04-11
2012-05-11
2012-06-10
Figure 8. Salinity at three USGS stations: 02291310, 02291315, 02291330
CH3D Model Setup
CH3D model was setup using the data previously described in the Data Assessment report. The CH3D model
is driven by following forcing: tide, wind and river flows. The model is run in a 3D mode using six vertical sigma
layers with Coriolis parameter calculated at the latitude in the middle of the domain: 26.0 degrees. Minimum
model depth was set to 150 cm, due to the fact that the tidal amplitudes on the East Coast of Florida can
exceed 1 meter and bathymetry data is relatively sparse, therefore bathymetry in some channels is not well
resolved.
The map of the domain and stations are shown in Figure 1 and the inshore portion of the domain is shown in
Figure 9, and approximate grid resolution is shown in Table 3.
Figure 9. Grid Mesh. Naples Bay Area
Table 3. CH3D model grid properties
Projection
Average cell size (inshore)
Average cell size (offshore)
UTM Zone 17, NAD 1983
~ 35 meters
~ 65 meters
Wind forcing
The wind forcing is based on two stations: the NOAA station #8725110 located near Naples, FL and the NERR
station located at Henderson Creek (Figure 1).
Open boundary condition (tides)
The open boundary condition is derived through calibration. Initially, a set of harmonic constituents is
obtained from NOAA (Table 4) and 10 major constituents (amplitude > 2cm) are selected, yielding the
following constituents: K1, O1, P1, Q1, K2, M2, N2, S2, SA and SSA. These constituents are used to specify the
open boundary conditions for the model. Adjustments are made to the constituents by running the model
simulation and comparing the constituents at the Naples NOAA station to the simulated results and making
necessary adjustments in the open boundary conditions to obtain good agreement at the Naples station.
Calibrated tidal constituents at the CH3D model open boundaries are listed in Table 5.
Table 4. Harmonic constituents at Naples, FL NOAA station. Amplitudes are in meters relative to MLLW.
Highlighted constituents are used as forcing at the open boundary of the model. Source:
http://tidesandcurrents.noaa.gov/harcon.html?id=8725110
Constituent #
Name
Amplitude
Phase
Speed
Description
1
M2
0.286
359.2
2
S2
0.096
6.1
3
N2
0.057
348.4
28.4397295 Larger lunar
constituent
4
K1
0.158
294.6
15.0410686 Lunar diurnal constituent
5
M4
0.017
193.6
57.9682084 Shallow water overtides of principal
lunar constituent
6
O1
0.143
293.0
13.9430356 Lunar diurnal constituent
7
M6
0.008
50.0
86.9523127 Shallow water overtides of principal
lunar constituent
8
MK3
0.009
101.8
44.0251729 Shallow water terdiurnal
9
S4
0.004
295.2
10
MN4
0.008
161.2
57.4238337 Shallow
water
constituent
11
NU2
0.013
359.7
28.5125831 Larger lunar evectional constituent
12
S6
0.0
0.0
13
MU2
0.009
275.3
27.9682084 Variational constituent
14
2N2
0.008
329.9
27.8953548 Lunar elliptical semidiurnal secondorder constituent
28.9841042 Principal lunar semidiurnal constituent
30.0
60.0
90.0
Principal solar semidiurnal constituent
elliptic
semidiurnal
Shallow water overtides of principal
solar constituent
quarter
diurnal
Shallow water overtides of principal
solar constituent
Constituent #
Name
Amplitude
Phase
Speed
Description
15
OO1
0.005
301.6
16
LAM2
0.002
2.4
17
S1
0.017
29.0
18
M1
0.008
321.5
14.4966939 Smaller lunar elliptic diurnal constituent
19
J1
0.01
289.9
15.5854433 Smaller lunar elliptic diurnal constituent
20
MM
0.0
0.0
0.5443747
Lunar monthly constituent
21
SSA
0.03
66.2
0.0821373
Solar semiannual constituent
22
SA
0.075
167.6
0.0410686
Solar annual constituent
23
MSF
0.0
0.0
1.0158958
Lunisolar synodic fortnightly constituent
24
MF
0.0
0.0
1.0980331
Lunisolar fortnightly constituent
25
RHO
0.006
292.1
13.4715145 Larger
lunar
constituent
26
Q1
0.03
282.4
13.3986609 Larger lunar elliptic diurnal constituent
27
T2
0.005
357.9
29.9589333 Larger solar elliptic constituent
28
R2
0.001
6.4
30.0410667 Smaller solar elliptic constituent
29
2Q1
0.004
263.3
12.8542862 Larger elliptic diurnal
30
P1
0.052
294.0
14.9589314 Solar diurnal constituent
31
2SM2
0.0
0.0
31.0158958 Shallow water semidiurnal constituent
32
M3
0.0
0.0
43.4761563 Lunar terdiurnal constituent
33
L2
0.008
39.1
29.5284789 Smaller lunar
constituent
34
2MK3
0.009
86.9
42.9271398 Shallow water terdiurnal constituent
35
K2
0.027
358.9
30.0821373 Lunisolar semidiurnal constituent
36
M8
0.0
0.0
37
MS4
0.008
217.2
16.1391017 Lunar diurnal
29.4556253 Smaller lunar evectional constituent
15.0
Solar diurnal constituent
evectional
elliptic
diurnal
semidiurnal
115.9364166 Shallow water eighth diurnal constituent
58.9841042 Shallow
water
constituent
quarter
diurnal
Table 5. Open boundary conditions at the open boundary of CH3D model domain. Amplitudes and phases
are relative to January 1, 2012 00:00.
Tidal constituent
K1
O1
P1
Q1
K2
M2
N2
S2
SA
SSA
Amplitude
47.7
5.7
9.6
2.7
14.3
15.8
5.2
3.0
7.5
3.0
Phase
-27.1
91.0
153.0
-51.1
179.8
-0.1
19.4
-40.2
171.1
226.5
River boundary conditions
The river boundary conditions are based on the flows at the stations identified on the map in Figure 1: GG1,
HC1, 1, 2, 3, 8, and 9. The GG1 and HC1 data are obtained from the DBHYDRO database, and other stations
are based on the estimated hydrological flows provided by Taylor Engineering / SFWMD.
Salinity boundary conditions
The salinity at river (flow) boundaries of CH3D model is set at 0 ppt (fresh water flow) as river boundaries are
sufficiently far from the inlet and there is no salt water intrusion at these points. At the open boundary of the
domain (offshore) different options were explored. Based on analysis of available data, such as regional model
results (HYCOM, NCOM) it was concluded that in the offshore the variation of salinity is very small (~ 0.3 ppt)
over the 6 months period and is even smaller (less than 0.1 ppt) at any instance of time over the CH3D
boundary in vertical and horizontal directions. Therefore, it was decided to use a single constant value at the
offshore open boundary of 35.5 ppt (average value over the time period of simulation).
Various model parameters not discussed here can be found in the main hydrodynamic input file for the CH3D
model that accompanies this report.
CH3D Model Simulation Results
Using the CH3D model and the model domain shown in Figure 1, test simulation results for the first six months
of 2012 are obtained. Results of water level and salinity are compared with measured data.
The following stations (Table 6) are selected to evaluate the model (refer to Figure 1 for station locations).
Table 6. List of stations selected for control of model results
Station Name
USGS 02291310 Gordon River at Rowing
Club Point Near Naples, FL
USGS 02291315 Naples Bay at City Dock
Near Naples, FL
USGS 02291330 Naples Bay at Gordon Pass
Near Naples, FL
8725110 Naples, FL
RBNERR LH
Lower Henderson Creek, FL
Location
26°08'57.9"N
81°47'09.98"W
26°07'57.96"N
81°47'34.19"W
26°05'35.28"N
81°47'53.31"W
26°7.9'N
81°48.4'W
26.02'57N
81.73'32W
Data Type
Water level,
salinity
Water level,
salinity
Water level,
salinity
Water level
Salinity
Frequency
Data
Source
15 min
USGS
15 min
USGS
15 min
USGS
6 min
15 min
NOAA
CDMO
Table 7 contains the statistical measures of model to data comparisons such as coefficient of determination
and root mean square and Figures 10-14 show the plots of measured and simulated data.
While water levels and salinity show reasonable agreement near the coast, the inland station 02291310
(Gordon River) (Error! Reference source not found.) shows some negative phase lag in water level, which
hould be addressed by further model calibration and verifying the bathymetry of the river to that point.
Salinity comparison at this station (Figures 13 and 14) shows considerable deviation as well, as measured data
shows significant stratification between the top and bottom, but model results show little stratification and
results match with data better at the top layer. It is possible that an increase in the number of layers would
help to improve the results (currently 4 vertical layers are used in the model).
Table 7. Coefficient of determination (r2) and root mean square error (RMSE) for measured and simulated
data at select stations
Station Name
USGS 02291310 Gordon River at Rowing
Club Point Near Naples, FL
USGS 02291315 Naples Bay at City Dock
Near Naples, FL
USGS 02291330 Naples Bay at Gordon Pass
Near Naples, FL
8725110 Naples, FL
USGS 02291310 Gordon River at Rowing
Club Point Near Naples, FL
USGS 02291315 Naples Bay at City Dock
Near Naples, FL
USGS 02291330 Naples Bay at Gordon Pass
Near Naples, FL
Water level, m (NAVD88)
0.5
Data Type
Water Level
r2
0.83
RMSE
8 cm
Water Level
0.87
9 cm
Water Level
0.90
6 cm
Water Level
Salinity
(bottom/top)
Salinity
(bottom/top)
Salinity
(bottom/top)
0.93
0.52
0.57
0.81
0.79
0.90
0.89
6 cm
8 ppt
Naples, FL (8725110)
6 ppt
2 ppt
Measured
Simulated
0
-0.5
-1
2012-01-14
2012-01-28
2012-02-11
2012-02-25
2012-03-10
Figure 10. Measured and simulated water level at NOAA station at Naples, FL
2012-03-24
Figure 11. Measured and simulated water level at USGS station 02291310 (Gordon River)
Measured (top)
Measured (bottom)
Simulated (top)
Simulated (bottom)
40
35
Salinity, ppt
30
25
20
15
10
2012-01-12
2012-02-11
2012-03-12
Figure 12. Measured and simulated salinity at USGS station 02291310 (Gordon River)
Measured (top)
Measured (bottom)
Simulated (top)
Simulated (bottom)
Salinity, ppt
35
30
25
20
15
2012-01-04
2012-01-08
Figure 13. Measured and simulated salinity at USGS station 02291310 (Gordon River), zoom-in.
Discussion and Recommendations for Future Work
The CH3D model was setup using boundary conditions and parameterizations defined above. Simulation of a
6-month period produced plausible results, with RMSE of salinity between 2 and 8 ppt, given the limitations
of available data. The model domain and setup were tailored such that the model execution time are in-line
with the time recommended by the sponsor and are less than one day per year of simulation (in serial mode
using a PC based on Intel Core i7 CPU). The model code uses about 1.5GB of memory during runtime. If the
model code is used on computers with lower single core performance but multiple CPUs or CPU cores
available, parallel model could be employed to keep the model performance in line with or to exceed the
recommended performance.
Based on the initial model simulation and several subsequent model sensitivity runs, we believe that the
following weaknesses currently exist in the model:



Bathymetry data – while there is a good bathymetric dataset available for the Naples Bay, the data
for the Rookery Bay is rather sparse and channels may not be represented correctly in the model,
thus causing incorrect flowrates through these channels.
Flowrates at river boundaries – the data provided by Taylor Engineering is limited to annually
averaged flows. Improved boundary conditions could significantly improve results of salinity
simulations.
Tidal boundary conditions – two of the tidal constituents, SA and SSA, have periods (~12 and ~6
months, respectively) that are comparable to or longer than the period of simulation, therefore
accuracy of calibration for these constituents could have significant error. A 2-4 year simulation would
be desirable to calibrate and verify these constituents.
CH3D Model Input Files
An archive with a set of CH3D input files accompanies this report the files include:
fort.4
fort.15
grid.gdep
fort.1301
fort.14
fort.73
Main CH3D model input file
Model grid (binary format)
Model grid (ascii text format)
Rivers and streams (flow boundary conditions)
Wind forcing
Initial conditions