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30 changes: 15 additions & 15 deletions docs/couple/modflow-demo.qmd
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Expand Up @@ -60,11 +60,11 @@ and volume-discharge relationships.
:::

A visual representation of this simplified conceptual schematization is given
in <a href="#fig-volume-depth">Figure 1</a> and <a href="#fig-volume-discharge">Figure 2</a>.
in @fig-volume-depth and @fig-volume-discharge.

<figure id="fig-volume-depth" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187665858-d01fd60f-f3c2-4662-af82-cf8acfbe169b.PNG" alt="Figure 1: Distribution of water depths over the primary, secondary, and tertiary system." style="max-width: 100%;"><figcaption>alt="Figure 1: Distribution of water depths over the primary, secondary, and tertiary system."</figcaption></figure>
![Distribution of water depths over the primary, secondary, and tertiary system.](https://user-images.githubusercontent.com/13662783/187665858-d01fd60f-f3c2-4662-af82-cf8acfbe169b.PNG){#fig-volume-depth}

<figure id="fig-volume-discharge" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187668931-c04d4126-9208-44f5-bafa-4c5f74a96dc9.PNG" alt="Figure 2: Discharge as a function of basin storage volume." style="max-width: 100%;"><figcaption>alt="Figure 2: Discharge as a function of basin storage volume."</figcaption></figure>
![Discharge as a function of basin storage volume.](https://user-images.githubusercontent.com/13662783/187668931-c04d4126-9208-44f5-bafa-4c5f74a96dc9.PNG){#fig-volume-discharge}

An example of the resulting parameters for a single cell is shown in
@tbl-hupsel-v-h. The first row shows the water levels when the basin is empty.
Expand All @@ -85,21 +85,21 @@ in the test cases for the sake of simplicity.

: Volume-level table for a single cell in the Hupsel basin. {#tbl-hupsel-v-h}

<a href="#fig-grid-volume">Figure 3</a> shows the volume of the first row of the cell based
@fig-grid-volume shows the volume of the first row of the cell based
input for the primary system. Symbology is set to unique values. While water
levels differ per cell in this parametrization, the "normative volume" defined
above is shared by all cells in a basin.

<figure id="fig-grid-volume" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187672671-20d22031-3b50-474a-9ee1-4408c25a4f30.PNG" alt="Figure 3: Basin normative volume of the primary system." style="max-width: 100%;"><figcaption>alt="Figure 3: Basin normative volume of the primary system."</figcaption></figure>
![Basin normative volume of the primary system.](https://user-images.githubusercontent.com/13662783/187672671-20d22031-3b50-474a-9ee1-4408c25a4f30.PNG){#fig-grid-volume}

<a href="#fig-grid-volume">Figure 3</a> shows the water level corresponding to the normative storage
@fig-grid-volume shows the water level corresponding to the normative storage
volume based input for the primary system (it corresponds to the value shown in
the first row of the primary column in @tbl-hupsel-v-h). We see a clear gradient
from west to east: as our simplified parametrization assumes a constant water
depth for all cells in a single system, water levels spatially fall and rise
with the bottom elevation.

<figure id="fig-grid-level" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187672663-99b9efd3-5e09-4d6f-bd3a-4180ff5b2ce4.PNG" alt="Figure 4: Water level corresponding to the normative basin volume of the primary system." style="max-width: 100%;"><figcaption>alt="Figure 4: Water level corresponding to the normative basin volume of the primary system."</figcaption></figure>
![Water level corresponding to the normative basin volume of the primary system.](https://user-images.githubusercontent.com/13662783/187672663-99b9efd3-5e09-4d6f-bd3a-4180ff5b2ce4.PNG){#fig-grid-level}

## Example: Configuration

Expand Down Expand Up @@ -169,9 +169,9 @@ From these tests, we expect the following behavior:
2. In case of negative recharge (evapotranspiration), infiltration occurs in the surface waters.
Infiltration should be zero when the basin volume is 0.

<figure id="fig-hupsel-gwb-steady" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187715341-fd99dc06-2eda-4b84-a201-650dc7220574.png" alt="Figure 5: Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d." style="max-width: 100%;"><figcaption>alt="Figure 5: Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d."</figcaption></figure>
![Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187715341-fd99dc06-2eda-4b84-a201-650dc7220574.png){#fig-hupsel-gwb-steady}

<a href="#fig-hupsel-gwb-steady">Figure 5</a> shows the water balance of steady-state for submodel of the
@fig-hupsel-gwb-steady shows the water balance of steady-state for submodel of the
LHM that has been by selecting the cells belonging to the district containing
the Hupsel catch, the Berkel.

Expand All @@ -194,9 +194,9 @@ steady-state model), the surface waters provide mostly inflow, and recharge is
a negative term. In this case, the secondary system provides a small amount of
infiltration; most of the water is drawn from the surroundings instead.

<figure id="fig-hupsel-gwb-volume0" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187715349-9eee8830-9b03-4a88-b7c9-b16004c694f6.png" alt="Figure 6: Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d." style="max-width: 100%;"><figcaption>alt="Figure 6: Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d."</figcaption></figure>
![Water balance of the MODFLOW 6 boundary conditions for the Hupsel basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187715349-9eee8830-9b03-4a88-b7c9-b16004c694f6.png){#fig-hupsel-gwb-volume0}

<a href="#fig-hupsel-gwb-volume0">Figure 6</a> shows the same model, with 0-basin volume which causes
@fig-hupsel-gwb-volume0 shows the same model, with 0-basin volume which causes
water levels to be set equal to bed elevation. Consequently, primary and
secondary outflow terms are larger for positive groundwater recharge as they
drain at a lower level and intercept the water before the tertiary system does.
Expand All @@ -215,9 +215,9 @@ process, but without Ribasim. This results in volumes of 0.0, so all MODFLOW 6
water levels are set equal to bed elevation.
3. A coupled run where the water levels are updated by Ribasim.

<figure id="fig-tol-gwb-steady" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187769185-f63a5821-dfe8-4d99-b43e-780962e73870.png" alt="Figure 7: Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d." style="max-width: 100%;"><figcaption>alt="Figure 7: Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d."</figcaption></figure>
![Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a standalone MODFLOW 6 run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187769185-f63a5821-dfe8-4d99-b43e-780962e73870.png){#fig-tol-gwb-steady}

<a href="#fig-tol-gwb-steady">Figure 7</a> shows the water balance of steady-state for a submodel of
@fig-tol-gwb-steady shows the water balance of steady-state for a submodel of
the LHM for the Polder de Tol and its surroundings. While groundwater recharge
is the dominant ingoing flow, lateral groundwater flow (over the entire depth
of the groundwater model) is a sizable inflow for the area; the larger lateral
Expand All @@ -228,9 +228,9 @@ ephemeral tertiary ditches, but by the permanently water-bearing ditches of the
primary and secondary system. Unlike the Hupsel, the water balance does not
shrink to very small discharges, as there is sizable regional groundwater flow.

<figure id="fig-tol-gwb-volume0" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187769180-91f6344c-3489-4200-8a0c-d5e82a28ebaf.png" alt="Figure 8: Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d." style="max-width: 100%;"><figcaption>alt="Figure 8: Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d."</figcaption></figure>
![Water balance of the MODFLOW 6 boundary conditions for De Tol basin for a zero volume run. The four sequential steady states (01, 02, 03, 04) use net groundwater recharge values of 1.0, 0.5, -0.05 and -0.1 mm/d.](https://user-images.githubusercontent.com/13662783/187769180-91f6344c-3489-4200-8a0c-d5e82a28ebaf.png){#fig-tol-gwb-volume0}

<a href="#fig-tol-gwb-volume0">Figure 8</a> shows the same model, with 0-basin volume which causes
@fig-tol-gwb-volume0 shows the same model, with 0-basin volume which causes
water levels to be set equal to bed elevation. The total discharge is larger:
the primary and secondary systems are set to lower levels, and so the head
difference is larger. While De Tol's evapotranspiration excess can be fed by
Expand Down
14 changes: 7 additions & 7 deletions docs/index.qmd
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Expand Up @@ -52,9 +52,9 @@ a set of symbolic equations, and can be connected to each other. From this a sim
system of equations is generated automatically. We use solvers with adaptive time stepping
from [DifferentialEquations.jl](https://diffeq.sciml.ai/stable/) to get results.

<figure id="None" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/4471859/179259333-070dfe18-8f43-4ac4-bb38-013b252e2e4b.png" alt="Figure 1: Example timeseries of a single basin, the Hupselse Beek, with the input and output fluxes on the top, and the storage volume (the state) below." style="max-width: 100%;"><figcaption>alt="Figure 1: Example timeseries of a single basin, the Hupselse Beek, with the input and output fluxes on the top, and the storage volume (the state) below."</figcaption></figure>
![Example timeseries of a single basin, the Hupselse Beek, with the input and output fluxes on the top, and the storage volume (the state) below.](https://user-images.githubusercontent.com/4471859/179259333-070dfe18-8f43-4ac4-bb38-013b252e2e4b.png)

<figure id="None" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/4471859/179259174-0caccd4a-c51b-449e-873c-17d48cfc8870.png" alt="Figure 2: Example bar plot of the daily waterbalance for the Hupselse Beek, comparing results of Mozart (left) and Ribasim (right)." style="max-width: 100%;"><figcaption>alt="Figure 2: Example bar plot of the daily waterbalance for the Hupselse Beek, comparing results of Mozart (left) and Ribasim (right)."</figcaption></figure>
![Example bar plot of the daily waterbalance for the Hupselse Beek, comparing results of Mozart (left) and Ribasim (right).](https://user-images.githubusercontent.com/4471859/179259174-0caccd4a-c51b-449e-873c-17d48cfc8870.png)


# Introduction
Expand Down Expand Up @@ -108,7 +108,7 @@ Local Surface Water (LSW)). Each basin has an associated polygon, and the set of
connected to each other as described by a graph, which we call the network. Below is a
representation of both on the map.

<figure id="None" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/4471859/185932183-62c305e6-bc14-4f3c-a74c-437f831c9145.png" alt="Figure 3: Mozart Local Surface Water polygons and their drainage." style="max-width: 100%;"><figcaption>alt="Figure 3: Mozart Local Surface Water polygons and their drainage."</figcaption></figure>
![Mozart Local Surface Water polygons and their drainage.](https://user-images.githubusercontent.com/4471859/185932183-62c305e6-bc14-4f3c-a74c-437f831c9145.png)

The network is described as graph. Flow can be bi-directional, and the graph does not have
to be acyclic.
Expand All @@ -131,16 +131,16 @@ lines between A, B, C, and D) instead.

Multiple basins may exist within the same spatial polygon, representing
different aspects of the surface water system (perennial ditches, ephemeral
ditches, or even surface ponding). <a href="#fig-p">Figure 4</a>, <a href="#fig-s">Figure 5</a>, <a href="#fig-t">Figure 6</a> show the 25.0 m
ditches, or even surface ponding). @fig-p, @fig-s, @fig-t show the 25.0 m
rasterized primary, secondary, and tertiary surface waters as identified by BRT
TOP10NL [@pdoktopnl] in the Hupsel basin (as defined in the Mozart LSW's).
These systems may represented in multiple ways.

<figure id="fig-p" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187625163-d0a81bb6-7f55-4ad1-83e2-90ec1ee79740.PNG" alt="Figure 4: Hupsel: primary surface water." style="max-width: 100%;"><figcaption>alt="Figure 4: Hupsel: primary surface water."</figcaption></figure>
![Hupsel: primary surface water.](https://user-images.githubusercontent.com/13662783/187625163-d0a81bb6-7f55-4ad1-83e2-90ec1ee79740.PNG){#fig-p}

<figure id="fig-s" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187625170-1acdfb41-7077-443f-b140-ae18cbf21e53.PNG" alt="Figure 5: Hupsel: secondary surface water." style="max-width: 100%;"><figcaption>alt="Figure 5: Hupsel: secondary surface water."</figcaption></figure>
![Hupsel: secondary surface water.](https://user-images.githubusercontent.com/13662783/187625170-1acdfb41-7077-443f-b140-ae18cbf21e53.PNG){#fig-s}

<figure id="fig-t" style="max-width: 100%;"><img src="https://user-images.githubusercontent.com/13662783/187625174-3eec28b5-ddbb-4870-94c3-d9e9a43f8eb4.PNG" alt="Figure 6: Hupsel: tertiary surface water." style="max-width: 100%;"><figcaption>alt="Figure 6: Hupsel: tertiary surface water."</figcaption></figure>
![Hupsel: tertiary surface water.](https://user-images.githubusercontent.com/13662783/187625174-3eec28b5-ddbb-4870-94c3-d9e9a43f8eb4.PNG){#fig-t}

As a single basin (A) containing all surface water, discharging to its
downstream basin to the west (B):
Expand Down
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