A quick tutorial on PHABSIM

INTRODUCTION
Two types of data are required to run the PHABSIM software:
1. Hydraulic-habitat data
i. Topographical information: cross-sectional X, Y, Z coordinates
ii. Stage-discharge curves for each cross section
iii. Manning’s roughness coefficient for each cross section
2. Biological data - habitat suitability curves for selected fish species or aquatic insects
(or riparian vegetation and aquatic macrophytes)

The purpose of a hydraulic habitat modelling application is to develop environmental

flow scenarios, usually downstream of hydrologically-altered river reaches. A river reach in
PHABSIM, and generally in 1-dimensional models is described using cross sections. PHABSIM
uses the cross-sectional hydraulic information to divide the study reach into segments (cells)
across each cross section. It then predicts the water depth (D) and depth-averaged flow velocity
(V) at each cell of each cross section in various simulated discharge (Q) scenarios. Finally, it
searches on the user-defined habitat suitability curves for selected aquatic organisms for the
values of V, D, substrate (S) and often temperature (T), which yield the highest habitat
suitability and calculates the Weighted Usable Area (see the presentation
‘Hydraulic_habitat_modelling_Theodoropoulos_2020’ for details) for each Q scenario. The Q
with the highest WUA is usually the environmental flow selected for the river reach (in real-life
cases however, a negotiated lower Q value may be applied).

INPUTTING THE HYDRAULIC-HABITAT DATA IN PHABSIM

Open the PHABSIM software and create a new project
File -> New Project
Enter your project name, browse to select the folder where your project will be stored (click
browse and select the folder you prefer). Give your project a short description and select
‘metric’ in order to use the SI unit system.

A. CROSS SECTIONS
Edit -> Cross sections
1. Press the down arrow to enter a new cross section - assign the cross section an ID
preferably using integers and starting from 1 for the most downstream cross section.
You may need to enter the ID two times to be set.
2. In the ‘Length’ column you enter the distance between the cross sections (CS)
(apparently the first CS will have a 0.000 distance). BE CAREFULL! It is the distance
between the neighboring CS (CS1 has always a 0.000 Length, the Length in CS2 will be
the distance of CS2 to CS1, the Length of CS3 will be the distance of CS3 to CS2 etc.).
3. Leave all other columns intact, except for
 i. SZF (Stage of Zero Flow) - It is the Water Surface Elevation in which the water
barely runs. Based on the PHABSIM manual, you can use the lowest Z value of the
cross section as the SZF.
ii. N (Manning’s roughness coefficient) - Usually varies from 0.03 to 0.07 or higher
and depends on the dominant substrate type at each CS.
iii. Slope - In a uniform flow, the energy slope equals the slope of the bottom, so
here you can input the slope of the bottom between the two CS (for the first CS
use a very small value instead of 0.000, or leave it at the default PHABSIM value).

B. COORDINATE DATA
Now that you have defined the number of the cross sections, their distance, N, slope and SZF,
you need to input their coordinates (X and Z since Y is automatically calculated as the distance
between each CS). Having the first CS selected, go to the ‘Coordinate Data’ tab. Press the down
arrow as many times as the coordinate pairs of X and Z you have to input. Probably you will
copy/paste these data from an excel worksheet but before copying/pasting, select the first
column that you created and right click -> fill (you can see the column filled with zeros). Now
copy and paste your coordinates. Press close. You have just entered the coordinates for the
first cross section. Now select the CS2 (Edit -> Cross Sections) and press Coordinate Data again.
Copy and paste the coordinates in the same way and do this for all your cross sections.

C. CALIBRATION DATA
In the same manner as with the Coordinate Data, select the first cross section and click on the
‘Calibration Data’ tab. Here you input the stage-discharge curve for each cross section (you
have to do it manually). Press the down arrow to enter a new Q and then enter the relevant
WSL for this Q. Stage and WSL means the same thing. The WSL is entered in the ‘User WSL’
column and the Q is entered in the ‘Best Est Q’ column. Usually you will have 3 or 4 stage-
discharge pairs to input. You should do this process for all your cross sections.

Now that you have entered the required hydraulic information, you must tell PHABSIM, which
discharges you would like to simulate. Select Edit -> Discharges. By pressing the down arrow
you add your preferred discharges (note that the Q you have already entered in the Calibration
Data are already there).

ENTERING THE HABITAT SUITABILITY CURVES

You can find habitat suitability curves available in the internet. They are plots of habitat
suitability against V, D, S and T. To input these plots in PHABSIM press Edit -> Suitability Curves.
In the window that pops up press Edit -> Add Curve, give it an ID (preferably an integer), name
the species and the life stage. Select the curve type (Velocity is selected by default) and press
the down arrow to start writing your data. Each ‘down arrow’ creates a row where you input
the Velocity and the relevant Suitability as you see it in the plot. Do the same for the Depth
curve. Regarding the curves of substrate and temperature, if you don’t have data just input
some classes with a suitability of 1 at each class.
Trick: PHABSIM requires the x axis of all habitat suitability curves to end with 100.000. So after
finishing entering the habitat suitability values, enter on more row with X value (velocity or
depth or channel index or temperature) = 100.000 and ‘Suitability’ = the same value with your
previous input.

RUNNING THE MODELS OF PHABSIM

Models -> WSL
This tab has several models to enable PHABSIM predict/model the WSL (and as a result the
water depth) at each simulated Q. Use the STGQ modelling method. Press STGQ - Set All - Run.
In the Results tab you can see the simulated WSLs for each cross section at each Q.

Models -> Velocity

This model enables PHABSIM to calculate/predict the flow velocity at each cross section using
the Manning’s equation and given the water depth (WSL) calculated before. Just press run and
see the results in the relevant tab.

Models -> Habtae

This model allows PHABSIM to compare the V and D values at each Q (and additionally S and T)
for each cross section with the habitat preferences of the selected species and derive the
highest and lowest suitability values. For each Q, PHABSIM calculates the WUA and then plots
the results. Before pressing Run, press Limits and select ‘No restrictions’ and ‘No minimum
factor specified’. Then go to ‘Life Stages’, select the one you want and go to ‘Output Options’
and press Run. You can see the Q - WUA plot in the ‘WUA Results’, by pressing Graph. And you
can also visualize your cross-sections output (the habitat suitability at each cell of each cross
section in the various discharges simulated) by going to ‘Habitat Results’ and pressing Graph.
Take your time to explore this final visualization graph as it is very well looking and may help
you when you need to show your output to water managers and stakeholders.

Finished!
If you are curious on how these models calculate everything, just consult the very detailed
PHABSIM manual.

Christos Theodoropoulos
If you need further assistance email me and Prof. Stamou at ctheodor@hcmr.gr and
stamou@central.ntua.gr respectively.