#### Estuarine salinity 1D model

##### Joao G. Ferreira ★

This model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the upper slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

The lower slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the upper slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

The lower slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

- 2 years 4 months ago

#### Forcing functions (tides and light)

##### Joao G. Ferreira ★

This very simple model generates a tidal curve and a light climate at the sea surface to illustrate the non-linearity of the diel and tidal cycles. This has repercussions on benthic primary (and therefore also secondary) production.

- 2 years 12 months ago

#### Estuarine salinity 1 box model (J. Gomes Ferreira)

##### Andre Simoes

This model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 4 years 9 months ago

#### Estuary Salinity 4 Boxes Model

##### Andre Simoes

This model represents the four-dimensional version of the advection-dispersion equation

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

At steady state

E(b)1,2 = QS1/(S1-S2)

**(1)**for an estuary.dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

**(1)**Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

**(2)**EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

**(2)**for the first estuarine box as:Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

**(3)**Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

**(4)**At steady state

E(b)1,2 = QS1/(S1-S2)

**(5)**- 4 years 9 months ago

#### Estuarine Nitrates 4 boxes model

##### Tiago Gageiro

[ This model represents the four-dimensional version of the advection-dispersion equation (1) for an estuary.

dN/dt = (1/A)d(QN)/dx - (1/A)d(EA)/dx(dN/dx) (1)

Where N: Nitrates (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdN/dt = QdN - (d(EA)/dx) dN (2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite (2) for the first estuarine box as:

Q(Nr-N1)=E(b)r,1(Nr-N1)-E(b)1,2(N1-N2) (3)

Where Sn: river nitrates(=5), N1: mean estuary Nitrates for box 1; N2: mean estuary nitrates for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Therefore:

QN1=E(b)1,2(N1-N2) (4)

At steady state

E(b)1,2 = QN1/(N1-N2) (5) ]

dN/dt = (1/A)d(QN)/dx - (1/A)d(EA)/dx(dN/dx) (1)

Where N: Nitrates (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdN/dt = QdN - (d(EA)/dx) dN (2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite (2) for the first estuarine box as:

Q(Nr-N1)=E(b)r,1(Nr-N1)-E(b)1,2(N1-N2) (3)

Where Sn: river nitrates(=5), N1: mean estuary Nitrates for box 1; N2: mean estuary nitrates for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Therefore:

QN1=E(b)1,2(N1-N2) (4)

At steady state

E(b)1,2 = QN1/(N1-N2) (5) ]

- 4 years 9 months ago

#### CREEK - Carrying Capacity of Oysters

##### Joao G. Ferreira ★

This model implements a very simple shellfish carrying capacity simulation for tidal creeks with freshwater input.

Physics

The model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the top slider to turn off dispersion (set to zero). If the variable being simulated is (a) salinity, you will see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system; (b) POM, then the ocean (which typically has less POM) will not contribute a flushing effect and the concentration of POM in the tidal creek or estuary will be higher.

The second slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

Biology

Two biological functions are implemented in CREEK, both extremely simplified.

1. Primary production - a constant primary production rate is considered in gC m-3 d-1

2. Oyster filtration - a constant clearance rate (CR) is considered in L ind- 1 h-1, scaled to a certain stocking density S (ind m-3)

Units are normalized, and food depletion is CR * S * POM, in g POM m-3 d-1

The third slider allows for adjustment of different aquaculture densities.

Wild filter-feeding species are included in the model, using an identical clearance rate to the cultivated oysters. Wild species can be turned on or off in the model using the fourth slider.

The model provides three outputs:

1. POM concentration in mg L-1

2. Equivalent in chlorophyll (ug L-1)

3. Total oyster biomass in kg for the whole system

Physics

The model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the top slider to turn off dispersion (set to zero). If the variable being simulated is (a) salinity, you will see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system; (b) POM, then the ocean (which typically has less POM) will not contribute a flushing effect and the concentration of POM in the tidal creek or estuary will be higher.

The second slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

Biology

Two biological functions are implemented in CREEK, both extremely simplified.

1. Primary production - a constant primary production rate is considered in gC m-3 d-1

2. Oyster filtration - a constant clearance rate (CR) is considered in L ind- 1 h-1, scaled to a certain stocking density S (ind m-3)

Units are normalized, and food depletion is CR * S * POM, in g POM m-3 d-1

The third slider allows for adjustment of different aquaculture densities.

Wild filter-feeding species are included in the model, using an identical clearance rate to the cultivated oysters. Wild species can be turned on or off in the model using the fourth slider.

The model provides three outputs:

1. POM concentration in mg L-1

2. Equivalent in chlorophyll (ug L-1)

3. Total oyster biomass in kg for the whole system

Environment Estuary Carrying Capacity Primary Production Hydrodynamics Salinity

- 3 months 2 weeks ago

#### Estuarine salinity 1D volume model

##### Joao G. Ferreira ★

This model implements the one-dimensional version of the advection-dispersion equation for an estuary.

It develops the basic 1D model by simulating the mass of salt rather than the concentration. This makes it straightforward to deal with multiple boxes of different volume.

The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the upper slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

The lower slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

It develops the basic 1D model by simulating the mass of salt rather than the concentration. This makes it straightforward to deal with multiple boxes of different volume.

The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the upper slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

The lower slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

- 10 months 2 weeks ago

#### Estuarine Salinity 4 boxes model

##### Tiago Gageiro

[ This model represents the four-dimensional version of the advection-dispersion equation (1) for an estuary.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (1) Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1). For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes: VdS/dt = QdS - (d(EA)/dx) dS (2) EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q) We can rewrite (2) for the first estuarine box as: Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2) (3) Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2. Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore: QS1=E(b)1,2(S1-S2) (4) At steady state E(b)1,2 = QS1/(S1-S2) (5) ]

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (1) Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1). For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes: VdS/dt = QdS - (d(EA)/dx) dS (2) EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q) We can rewrite (2) for the first estuarine box as: Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2) (3) Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2. Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore: QS1=E(b)1,2(S1-S2) (4) At steady state E(b)1,2 = QS1/(S1-S2) (5) ]

- 4 years 9 months ago

#### Clone of CREEK - Carrying Capacity of Oysters

##### Nancy Hadley

This model implements a very simple shellfish carrying capacity simulation for tidal creeks with freshwater input.

Physics

The model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the upper slider to turn off dispersion (set to zero). If the variable being simulated is (a) salinity, you will see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system; (b) POM, then the ocean (which typically has less POM) will not contribute a flushing effect and the concentration of POM in the tidal creek or estuary will be higher.

The middle slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

Biology

Two biological functions are implemented in CREEK, both extremely simplified.

1. Primary production - a constant primary production rate is considered in gC m-3 d-1

2. Oyster filtration - a constant clearance rate (CR) is considered in L ind- 1 h-1, scaled to a certain stocking density S (ind m-3)

Units are normalized, and food depletion is CR * S * POM, in g POM m-3 d-1

The lower slider allows for adjustment of different densities.

The model provides three outputs:

1. POM concentration in mg L-1

2. Equivalent in chlorophyll (ug L-1)

3. Total oyster biomass in kg for the whole system

Physics

The model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the upper slider to turn off dispersion (set to zero). If the variable being simulated is (a) salinity, you will see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system; (b) POM, then the ocean (which typically has less POM) will not contribute a flushing effect and the concentration of POM in the tidal creek or estuary will be higher.

The middle slider allows you to simulate a variable river flow, and understand how dispersion compensates for changes in freshwater input.

Biology

Two biological functions are implemented in CREEK, both extremely simplified.

1. Primary production - a constant primary production rate is considered in gC m-3 d-1

2. Oyster filtration - a constant clearance rate (CR) is considered in L ind- 1 h-1, scaled to a certain stocking density S (ind m-3)

Units are normalized, and food depletion is CR * S * POM, in g POM m-3 d-1

The lower slider allows for adjustment of different densities.

The model provides three outputs:

1. POM concentration in mg L-1

2. Equivalent in chlorophyll (ug L-1)

3. Total oyster biomass in kg for the whole system

Environment Estuary Carrying Capacity Primary Production Hydrodynamics Salinity

- 9 months 3 weeks ago

#### Clone of Estuarine salinity 1 box model (J. Gomes Ferreira)

##### João Serra

This model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 10 months ago

#### Clone of Clone of Estuarine salinity 1 box model (J. Gomes Ferreira)

##### João Serra

This model implements the one-dimensional version of the advection-dispersion equation for an estuary. The equation is:

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 9 months ago

#### Clone of Estuarine salinity 1 box model (J. Gomes Ferreira)

##### João Serra

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 10 months ago

#### Clone of Estuarine salinity 1 box model (J. Gomes Ferreira)

##### João Serra

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 10 months ago

#### Clone of Clone of Estuarine salinity 1 box model (J. Gomes Ferreira)

##### João Serra

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 9 months ago

#### Clone of Estuary Salinity 4 Boxes Model

##### João Serra

This model represents the four-dimensional version of the advection-dispersion equation

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

At steady state

E(b)1,2 = QS1/(S1-S2)

**(1)**for an estuary.dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

**(1)**Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

**(2)**EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

**(2)**for the first estuarine box as:Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

**(3)**Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

**(4)**At steady state

E(b)1,2 = QS1/(S1-S2)

**(5)**- 3 years 9 months ago

#### Clone of Estuarine salinity 1D model

##### João Serra

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 9 months ago

#### Clone of Clone of Clone of Estuarine salinity 1 box model (J. Gomes Ferreira)

##### João Serra

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 9 months ago

#### Clone of Estuarine salinity 1 box model (J. Gomes Ferreira)

##### João Serra

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 9 months ago

#### Clone of Estuary Salinity 4 Boxes Model

##### João Serra

This model represents the four-dimensional version of the advection-dispersion equation

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

At steady state

E(b)1,2 = QS1/(S1-S2)

**(1)**for an estuary.dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

**(1)**Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

**(2)**EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

**(2)**for the first estuarine box as:Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

**(3)**Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

**(4)**At steady state

E(b)1,2 = QS1/(S1-S2)

**(5)**- 3 years 9 months ago

#### Clone of Estuary Salinity 4 Boxes Model

##### João Serra

**(1)**for an estuary.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

**(1)**

Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

**(2)**

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

**(2)**for the first estuarine box as:

Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

**(3)**

Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

**(4)**

At steady state

E(b)1,2 = QS1/(S1-S2)

**(5)**

- 3 years 9 months ago

#### Clone of Estuary Salinity 4 Boxes Model

##### João Serra

**(1)**for an estuary.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

**(1)**

Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

**(2)**

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

**(2)**for the first estuarine box as:

Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

**(3)**

Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

**(4)**

At steady state

E(b)1,2 = QS1/(S1-S2)

**(5)**

- 3 years 9 months ago

#### Clone of Estuary Salinity 4 Boxes Model

##### João Serra

**(1)**for an estuary.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

**(1)**

Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

**(2)**

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

**(2)**for the first estuarine box as:

Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

**(3)**

Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

**(4)**

At steady state

E(b)1,2 = QS1/(S1-S2)

**(5)**

- 3 years 9 months ago

#### Clone of Estuarine salinity 1D model

##### João Serra

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx) (Eq. 1)

Where S: salinity (or any other constituent such as chlorophyll or dissolved oxygen), (e.g. kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume. For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS (Eq. 2)

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient, units in m3 s-1, i.e. a flow, equivalent to Q

At steady state, dS/dt = 0, therefore we can rewrite Eq. 2 for one estuarine box as:

Q(Sr-Se)=E(b)r,e(Sr-Se)-E(b)e,s(Se-Ss) (Eq. 3)

Where Sr: river salinity (=0), Se: mean estuary salinity; Ss: mean ocean salinity

E(b)r,e: dispersion coefficient between river and estuary, and E(b)e,s: dispersion coefficient between the estuary and ocean.

By definition the value of E(b)r,e is zero, otherwise we are not at the head (upstream limit of salt intrusion) of the estuary. Likewise Sr is zero, otherwise we're not in the river. Therefore:

QSe=E(b)e,s(Se-Ss) (Eq. 4)

At steady state

E(b)e,s = QSe/(Se-Ss) (Eq 5)

The longitudinal dispersion simulates the turbulent mixiing of water in the estuary during flood and ebb, which supplies salt water to the estuary on the flood tide, and make the sea a little more brackish on the ebb.

You can use the slider to turn off dispersion (set to zero), and see that if the tidal wave did not mix with the estuary water due to turbulence, the estuary would quickly become a freshwater system.

- 3 years 10 months ago

#### Clone of Estuary Salinity 4 Boxes Model

##### João Serra

**(1)**for an estuary.

dS/dt = (1/A)d(QS)/dx - (1/A)d(EA)/dx(dS/dx)

**(1)**

Where S: salinity (kg m-3); t: time (s); A: cross-sectional area (m2); Q: river flow (m3 s-1); x: length of box (m); E: dispersion coefficient (m2 s-1).

For a given length delta x, Adx = V, the box volume.For a set value of Q, the equation becomes:

VdS/dt = QdS - (d(EA)/dx) dS

**(2)**

EA/x, i.e. (m2 X m2) / (m s) = E(b), the bulk dispersion coefficient (m3 s-1, i.e. a flow, equivalent to Q)

We can rewrite

**(2)**for the first estuarine box as:

Q(Sr-S1)=E(b)r,1(Sr-S1)-E(b)1,2(S1-S2)

**(3)**

Where Sr: river salinity (=0), S1: mean estuary salinity for box 1; S2: mean estuary salinity for box 2; E(b)r,1: dispersion coefficient between river and estuary box 1; and E(b)1,2: dispersion coefficient between the estuary boxes 1 and 2.

Because we're at the head of the estuary, E(b)r,1 is zero, wich means: no salt enters the river. Sr is also zero, because the river salinity is zero. Therefore:

QS1=E(b)1,2(S1-S2)

**(4)**

At steady state

E(b)1,2 = QS1/(S1-S2)

**(5)**

- 3 years 9 months ago