Iber v3. Reference manual and GUI. Large wood transport calculation module


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==Iber v4. Reference manual and GUI. Instream large wood transport calculation module==

Virginia Ruiz-Villanueva<sup>1</sup>, Marcos Sanz-Ramos<sup>2</sup>, Ernest Bladé<sup>2</sup>

<sup>1</sup>Geomorphology, Natural Hazards and Risks Research Unit, Institute of Geography, Oeschger Centre for Climate Change Research (OCCR), University of Bern, Bern, Switzerland.

<sup>2</sup>Flumen Institute, Universitat Politècnica de Catalunya (UPC - Barcelona TECH) – International Centre of Numerical Methods in Engineering (CIMNE), 08034 Barcelona, Spain.

<span id='_Hlk204064138'></span>''Correspondence to'': [mailto:virginia.ruiz@unibe.ch virginia.ruiz@unibe.ch]

<br/>

<span id='_Toc204064700'></span>
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==Abstract==

Instream large wood plays a vital role in river systems, shaping habitats and supporting biodiversity. However, during floods, large wood transport can threaten infrastructure and communities. Traditional flood models often overlook wood material, despite its natural presence in rivers. To address this gap, the calculation module Iber-Wood was developed and integrated into the Iber model. Iber-Wood combines the Eulerian Iber 2D hydrodynamics with a Lagrangian model to simulate wood as dynamic elements. The model accounts for wood-flow-sediment, wood-wood, wood-infrastructure, and wood-terrain interactions, using two-way coupling. It has been validated with flume experiments and applied to various real rivers using field data. Applications include studying wood-sediment-flow dynamics and bridge-related wood accumulation. Though deterministic, Iber-Wood enables scenario testing and hypothesis exploration for complex wood dynamics.

'''Keywords: '''large wood, clogging, driftwood, woodjam, wood regime.

<span id='_Toc204064701'></span>

==Resumen==

<span id='_Hlk204088521'></span>El material leñoso de gran tamaño (troncos, restos de árboles, ramas y raíces) en los ríos desempeña un papel vital en los sistemas fluviales, configurando hábitats y sustentando la biodiversidad. Sin embargo, durante las inundaciones, el transporte de madera puede amenazar infraestructuras y comunidades. Los modelos de inundación tradicionales pasan por alto el transporte de material de madera, a pesar de su presencia natural en los ríos. Para abordar esta problemática, se desarrolló el módulo de cálculo Iber-Wood, que está completamente integrado en Iber. Iber-Wood combina la hidrodinámica euleriana 2D de Iber con un modelo lagrangiano para simular la madera como elementos dinámicos. El modelo considera las interacciones madera-flujo-sedimento, madera-madera, madera-infraestructura y madera-terreno, utilizando acoplamiento bidireccional. Se ha validado con experimentos de canal y se ha aplicado a varios ríos reales utilizando datos de campo. Las aplicaciones incluyen el estudio de la dinámica del flujo madera-sedimento y la acumulación de madera relacionada con los puentes. Aunque determinista, Iber-Wood permite la exploración de escenarios e hipótesis para dinámicas complejas de la madera.

<span id='_Hlk204088569'></span>'''Palabras clave: '''material leñoso, obstrucción, madera flotante, acumulación de madera, bloqueo de puente, régimen de la madera.

<br/><span id="_Toc204064702"></span>

==1. Introduction==
<span id="_Toc204064703"></span>

==='''1.1.''' Wood transport in rivers and wood transport modelling===

Wood significantly influences the hydraulics, morphodynamics, and ecology of fluvial systems, playing a key role in biodiversity support. However, during floods, large wood transport can pose substantial risks to infrastructure and communities. While models for flows and floods in mountain rivers have existed for decades, they often exclude organic material [<span id='cite-_Bib001'></span>[[#_Bib001|1]]], despite forested catchments naturally contributing substantial wood to rivers (e.g., uprooted trees and trunks). To address this, Iber-Wood was developed in 2013 [<span id='cite-_Bib002'></span>[[#_Bib002|2]]] and fully integrated into the Iber modelling framework [<span id='cite-_Bib003'></span>[[#_Bib003|3]],<span id='cite-_Bib004'></span>[[#_Bib004|4]],<span id='cite-_Bib005'></span>[[#_Bib005|5]]].

Iber-Wood couples 2D hydrodynamics and morphodynamics (Eulerian) with a Lagrangian discrete element model representing wood as cylindrical elements (with/without roots). These elements respond to hydrodynamic forces, enabling them to float, slide or drag, collide (inelastically), deposit, or remobilize. They interact with each other, with infrastructures, and the topography. The model is two-way coupled, meaning that the presence of wood modifies hydrodynamics by introducing a drag component into the Saint-Venant equations, thereby influencing morphodynamic processes; and the hydrodynamics govern the motion of wood. For details regarding the governing equations please see the reference [<span id='cite-_Bib006'></span>[[#_Bib006|6]]].

The model has been validated with flume experiments and applied to several rivers with field data [<span id='cite-_Bib007'></span>[[#_Bib007|7]],<span id='cite-_Bib008'></span>[[#_Bib008|8]],<span id='cite-_Bib009'></span>[[#_Bib009|9]],<span id='cite-_Bib010'></span>[[#_Bib010|10]],<span id='cite-_Bib011'></span>[[#_Bib011|11]]]. It has been used to study flow-wood-sediment interactions, where wood input alters sediment transport dynamics, and erosion can remobilize deposited wood [<span id='cite-_Bib003'></span>[[#_Bib003|3]],<span id='cite-_Bib012'></span>[[#_Bib012|12]]]. Applications include assessing wood accumulation at bridges and associated scour/aggradation [<span id='cite-_Bib013'></span>[[#_Bib013|13]],<span id='cite-_Bib014'></span>[[#_Bib014|14]]].

Despite its capabilities, Iber-Wood remains a deterministic model aiming at simulating a quasi-stochastic process, inherently subject to uncertainties. Accurate site-specific data and detailed observations are essential for model calibration and validation. Nevertheless, its main strength lies in the capacity to explore hypotheses and simulate multiple scenarios, offering valuable insights into complex, rarely observable wood dynamics.

<span id='_Hlk512499534'></span>''Please read the Iber documentation (i.e., quick user guide, hydraulic reference manual, tutorials and scientific papers) available at ''[http://www.iberaula.es ''www.iberaula.es'']'' for details. This document does not explain how to use Iber and assumes that the modeller is already familiar with the software. ''

The Iber online manual can be found here:

:* [https://www.scipedia.com/public/Sanz-Ramos_et_al_2022b Iber v3. Reference manual and GUI of the new implementations (in Spanish)]

As well as tutorials and benchmarks:

:* [https://doi.org/10.17979/spudc.9788497497176 Iber applications basic guide]
:* [https://doi.org/10.17979/spudc.9788497497640 Benchmarking of the Iber capabilities for 2D free surface flow modelling]
:* [https://drive.google.com/file/d/1qzvQ8J1wpFwRntfjggBKvheDTvzpuOAB/view River flood hazard modelling and management]
==='''1.2.''' This manual and Iber-Wood Installation===

This manual is a quick-start user guide for '''Iber version 3.4 or later'''. Further information, such as a description of the governing equations and applications, can be found in the References.

Iber-Wood is a calculation module (Plugin) of Iber, a freely distributed software for the simulation of free surface water flows. The interface of Iber is based on GiD, a pre- and post-process tool for multidimensional problem types. Therefore, the first step is to download and install Iber, available from: [https://www.iberaula.es/ https://www.iberaula.es/]

Once installed, Iber Wood can be activated in the menu '''Iber tools >> Plug-ins...''', as shown in Figure 1, and the Wood Transport can be turned on in the Data Window:

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 
{|
|-
| [[Image:Draft_Ruiz-Villanueva_363145736-image1.png|150px]]
| [[Image:Draft_Ruiz-Villanueva_363145736-image2.png|center|246px]]
|}
</div>

'''Figure 1: Activation window and general options for wood transport'''

Problem Data > Wood > Extra Results: additional results can be displayed; they have been used by the model developers mostly and are not needed for most users.<span id="_Toc204064704"></span>


==2. Pre-process: setting up a model==

Before defining the initial and/or boundary conditions for wood transport, the model setup must follow several key steps:

:* Create or import the computational geometry (optional)
:* Generate the computational mesh
:* Define input parameters (e.g., bed roughness, turbulence model)
:* Specify boundary (inflow/outflow) and initial conditions
:* Configure problem settings (e.g., simulation duration, numerical scheme parameters, additional module requirements)

Detailed guidance on each of these steps can be found in the corresponding model manuals.

''It is essential to ensure that all necessary data is available for running, validating, and calibrating the model. ''

If a model has been built with an older version of Iber or Iber-Wood is recommended to transform it to the latest version as shown in fFgure 2:

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image3.png|336px|alt=''''Figure 2: Transform tool for older projects''''|'''Figure 2: Transform tool for older projects''']] </div>

'''Figure 2: Transform tool for older projects'''

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==='''2.1.''' Wood input parameters and initial conditions===

The wood computation parameters, characteristics and initial conditions can be added in the Problem Data menu, Wood (Fig.3):

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image4.png|516px|alt=''''Figure 3: Wood data window with input parameters and initial conditions''''|'''Figure 3: Wood data window with input parameters and initial conditions''']] </div>

'''Figure 3: Wood data window with input parameters and initial conditions'''

[[Image:Draft_Ruiz-Villanueva_363145736-image5.png|24px]] Use the help button, place the mouse on some parameters and options to read more details and descriptions.


====Kinematic or dynamic approach====

The incipient motion of a log is fully dynamic, and it is based on the balance of forces (i.e., gravity, friction and drag forces) acting on the centre of mass of the log (i.e., wood piece). However, the velocity of the log can be simulated using two different approaches: kinematic and dynamic. In the first one, the kinematic approximation, log density, log diameter and water depth are used to define the transport regimes: resting, floating, or by traction (i.e., sliding). If the log floats ,the velocity is the same as the flow velocity, unless turbulence is included in the calculation (see section about turbulence). If the log slides on the river bed , the log velocity is different fromthe flow velocity.

The dynamic approximation uses the equations describing the movement of a rigid solid to calculate log velocity at each time step. In the case of the dynamic framework, the drag coefficient (Cd) used in the governing equations, has a strong influence on the resulted log velocity.

''We recommend using the kinematic approach, as it has undergone more extensive validation compared to the alternative dynamic method. Its reliability has been demonstrated across a wider range of scenarios and case studies.''

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====Drag Coefficient====

The drag coefficient is an important parameter in log velocity computations. This coefficient varies with the log shape, its position in the stream and Reynolds number. Drag coefficient values for many different shapes of bodies have been studied extensively. Here we reported some values:

{| style="width: 75%;margin: 1em auto 0.1em auto;border-collapse: collapse;" 
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Drag Coefficient Cd'''</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Reference'''</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Comments'''</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1.2</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Brooks et al., 2006</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Real logs</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1.41</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Bocchiola et al., 2006</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Dowels in flume</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">0.8</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Mazzorana et al., 2011</span>
|  style="border: 1pt solid black;text-align: center;"|
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">0.7-0.9</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Shields and Gippel, 1995</span>
|  style="border: 1pt solid black;text-align: center;"|
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1.5</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Alonso, 2004</span>
|  style="border: 1pt solid black;text-align: center;"|
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">0.4-1.2</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Gippel et al., 1996</span>
|  style="border: 1pt solid black;text-align: center;"|
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Fischerich and Morrow, 2000</span>
|  style="border: 1pt solid black;text-align: center;"|
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1.54</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Boothroyd et al., 2016</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Complex vegetation</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Up to 4</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Hui et al., 2010</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Leafy shrubs</span>
|}


<span id='_Hlk512500228'></span>''A constant value of 1.2 is suggested by default in the model but this value can be changed by the modeller and must be calibrated. ''

Additionally, a variable drag coefficient with log orientation (θ) can also be used. The equation proposed by Gippel (1992) is implemented in the model: 

''Cd=1.1173 - 5.28x10<sup>-2</sup>· Ɵ + 1.4385x10<sup>-3</sup>· Ɵ<sup>2 </sup>- 9.7668x10<sup>-6</sup>· Ɵ<sup>3</sup>''

<span id='_Toc204064707'></span>
====Friction Coefficient====

The other input parameter is the friction coefficient between the wood and the river bed. This value may significantly affect the movement of sliding logs; therefore, it must also be selected with caution.

''A value equal to 0.47 is used by default ''as suggested by Ishikawa (1989), although higher values were proposed by other authors:

{| style="width: 57%;margin: 1em auto 0.1em auto;border-collapse: collapse;" 
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Friction coefficient µ<sub>bed</sub>'''</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Reference'''</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">0.47</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Ishikawa, 1989</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">0.62</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Buxton, 2010</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">0.2</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Bocchiola et al., 2006</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Mazzorana et al., 2011</span>
|}


Additionally, the friction coefficient can be calculated as µ<sub>bed</sub>=tan(Ø), where Ø is the internal friction angle of soil.

<span id='_Toc204064708'></span>
====The wall bouncing angle====

The wall bouncing angle is used to compute log motion when logs touch a wall or a steep bank. When the incidence angle (i.e., the angle between the log and the boundary) is lower than this wall bouncing angle the movement of the log is treated as sliding or gliding parallel to the wall. On the other hand, if the incidence angle is higher, the log bounces off and changes its trajectory suddenly.

''Based on our own observations, we suggest a wall bouncing angle equal to 45º (0.78 radians). ''<span id="_Toc204064709"></span>


====Restitution Coefficient====

The Restitution Coefficient is used to compute the log-log interactions. Log-log interactions are considered as rigid bodies' elastic collisions when the Restitution Coefficient is equal to 1. Collisions might be inelastic by changing the value of the restitution coefficient.<span id="_Toc204064710"></span>


====Wood density====

Wood density is used to calculate the initial motion, and it influences the way logs move (floating or by traction). Wood density varies as a function of several factors, including tree species, wood type (proportion of early to late wood), tree age (and proportion of heartwood to sapwood), decay status, and moisture content.

''Therefore, wood density needs to be chosen with caution. ''

Some values reported in the literature are compiled in this table:

{| style="width: 100%;margin: 1em auto 0.1em auto;border-collapse: collapse;" 
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Wood density value or ranges (kg/m3)'''</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Comments'''</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">'''Reference'''</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">440-630</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Dry wood</span>
|  rowspan='2' style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Haga et al., 2007</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1150-1170</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Wet wood</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">1058</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Wet (saturated) wood</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Buxton, 2010</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">750</span>
|  style="border: 1pt solid black;text-align: center;"|
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Merten et al., 2010</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">693±102</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Abies (green wood)</span>
|  rowspan='9' style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Ruiz-Villanueva et al. (2016c) [<span id='cite-_Bib015'></span>[[#_Bib015|15]]]</span>


|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">794±79</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Acer (green wood)</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">874±73</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Alnus (green wood)</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">816±70</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Fraxinus (green wood)</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">793±118</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Populus (green wood)</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">843±150</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Quercus (decayed)</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">789±10</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Salix (decayed)</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">800</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Green wood</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">660</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Decayed instream wood</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">850-950</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Large Alders</span>
|  rowspan='2' style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Ruiz-Villanueva et al. (2016b,d) [<span id='cite-_Bib09'></span>[[#_Bib09|9]],<span id='cite-_Bib016'></span>[[#_Bib016|16]]]</span>
|-
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">400-700</span>
|  style="border: 1pt solid black;text-align: center;"|<span style="text-align: center; font-size: 75%;">Willows (Salix)</span>
|}


When logs are in contact with the water, they gain moisture, which influences the wood density. Based on experimental experience [<span id='cite-_Bib015'></span>[[#_Bib015|15]]], wood density may vary with time following the equation:

<big>''ρ<sub>f</sub> = ρ<sub>i</sub>∙e<sup>K·t</sup>''</big>

Where ''ρ<sub>f</sub>'' is the final wood density, ''ρ<sub>i</sub>'' is the initial wood density, ''K ''is a constant and ''t'' is time.

''For short time periods (i.e., flash floods), the variability in wood density due to moisture absorption might not be significant and can be neglected. ''

<span id='_Toc204064711'></span>
====Wood initial conditions or deposited logs====

Deposited logs, or initial conditions for wood, can be defined by specifying the following parameters for each log at a given time step (typically the initial one):

:* Position: x and y coordinates of the log’s centre of mass
:* Orientation: angle relative to the flow direction (in radians)
:* Length (m) and diameter (m)
:* Wood density (kg/m³)

Each log must be assigned a unique identification number.

If variable wood density is considered, the table also requires the initial density and a variation exponent (K) for each log.

Input data can be copied and pasted directly from a text file or an Excel spreadsheet.

====Wood with roots====

If logs include roots, this option must be enabled. Root systems are modelled as attached cylindrical elements [<span id='cite-_Bib011'></span>[[#_Bib011|11]]], defined by their maximum diameter and width. A reduction coefficient is then applied to adjust the effective size of each rootward.

The presence of roots affects the friction, gravity and drag forces acting on the log. The main effect of the presence of roots is the increase in resisting forces, as roots may contact the riverbed, increasing the friction, depending on the buoyancy. Furthermore, rooted pieces are more likely to rotate, with the roots pointing upstream [<span id='cite-_Bib017'></span>[[#_Bib017|17]]]. Our approximation only considers the frontal area of the rootwad, which has been proven to be the relevant parameter influencing the motion of wood with roots [<span id='cite-_Bib018'></span>[[#_Bib018|18]]].

<span id='_Toc204064712'></span>
==='''2.2.''' Wood boundary conditions and wood gauges===

Wood inlet boundary conditions and wood gauges can be assigned to the domain in the Data menu (Fig.4), and inlet boundary and initial conditions too (Fig.5).

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image6.png|396px|alt=''''Figure 4: Wood inlet boundary conditions and wood gauges menus''''|'''Figure 4: Wood inlet boundary conditions and wood gauges menus''']] </div>

'''Figure 4: Wood inlet boundary conditions and wood gauges menus'''

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image7.png|318px|alt=''''Figure 5: Inlet wood boundary conditions menu''''|'''Figure 5: Inlet wood boundary conditions menu''']] </div>
 

'''Figure 5: Inlet wood boundary conditions menu'''


Based on the modeller's knowledge of the fluvial corridor, riparian vegetation, and wood availability, ranges of maximum and minimum log lengths, diameters, root size and density of wood are defined. Stochastic variations of these parameters, together with the angle, are used to characterise each log entering the model.

Inlet boundary conditions (i.e., wood rate or flux: number of logs entering the simulation; Fig.6) can be assigned to the simulation domain boundaries (as many as needed), specifying a number of wood pieces per minute and their main characteristics (i.e., size and density). If more than one wood inlet is added, they should be numbered (e.g., Inlet number: 1, 2, 3…., n).

:* Wood inlet boundary conditions must be located at boundaries with inlet boundary conditions of flow
:* Wood rate is distributed proportionally to discharge across the inlet boundary
:* The entry log position along the boundary is randomly selected, but its probability is proportional to discharge
:* The end of the wood flux must be indicated with a value equal to 0

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image8.png|234px|alt=''''Figure 6: inlet boundary wood rate window''''|'''Figure 6: inlet boundary wood rate window''']] </div>
 

'''Figure 6: inlet boundary wood rate window'''


'''Wood gauges''' can be added at any place in the domain (once the mesh has been created), as a line perpendicular to the channel, to obtain the fluxes of wood in terms of logs (in number and volume) crossing the gauge at each time step (Fig. 7).

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image9.png|168px|alt=''''Figure 7: Wood gauge window''''|'''Figure 7: Wood gauge window''']] </div>

'''Figure 7: Wood gauge window'''

''Make sure the coordinates are entered correctly (edit them in the start and end points manually if needed, and be aware that GID writes these numbers in scientific notation).''<span id="_Toc204064713"></span>


==='''2.3.''' Turbulence===

Iber includes several turbulence models (i.e., constant viscosity coefficient, parabolic, mixing length and k–ε), but when considering the influence of turbulence on wood transport, only the Rastogi–Rodi k–ε model can be used so far (Fig.8). If turbulence is activated in the calculation, wood velocity is then calculated using the fluctuations of the turbulent flow velocity, which basically means introducing a random component into the motion of logs transported by a turbulent flow. In this way, identical logs dropped into the same spot may end up in different places.

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image10-c.png|132px|alt=''''Figure 8: Turbulence mode activated, compatible with wood transport.''''|'''Figure 8: Turbulence mode activated, compatible with wood transport.''']] </div>

'''Figure 8: Turbulence mode activated, compatible with wood transport.'''

''Please check the Iber documentation to learn more about the turbulence module.''

<span id='_Toc204064714'></span>
==='''2.4.''' Infrastructures===

Iber-Wood reproduces interactions between wood logs and infrastructures, computing whether a log can pass under or above a bridge deck, weir or gate, or become trapped by the structure. Interactions between wood and culverts or lids are not yet implemented.

''Please check the Iber documentation to learn how to add bridges, piers, weirs, gates, etc.''

<span id='_Toc204064715'></span>
==3. Computation==

To launch a computation, all the input parameters must be set.

The computation is starting with the menu Calculate (Fig.9).

''Please, read the Iber documentation regarding the calculation parameters, the results selection, etc.''

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image11-c.png|348px|alt=''''Figure 9: The menu Calculate''''|'''Figure 9: The menu Calculate''']] </div>

'''Figure 9: The menu Calculate'''

''View process info shows the progress of the calculation and the inlet and outlet discharge.''<span id="_Toc204064716"></span>


==4. Postprocess==

Once the computation is over, or even during the simulation process, the post-process interface can be accessed to visualise and analyse the results.

Switching between pre-processing and postprocessing interfaces can be done in the menu:

File > Post-process.

Or using the icon in the upper right:  [[Image:Draft_Ruiz-Villanueva_363145736-image12.png|24px|alt='''Iber provides multiple options to visualise and analyse the results; please check the Iber documentation. '''|''Iber provides multiple options to visualise and analyse the results; please check the Iber documentation. '']]

''Iber provides multiple options to visualise and analyse the results; please check the Iber documentation. ''

In the case of Iber-Wood, results can be displayed and visualised using the View Results menu (Fig.10).

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image13-c.png|174px|alt=''''Figure 10: View Results menu for wood''''|'''Figure 10: View Results menu for wood''']] </div>

'''Figure 10: View Results menu for wood'''

Different options are available to visualise the wood transport results at each time step: log visualisation (as lines), log density, number of logs, log velocity, etc.

Additional possibilities for the pre- and post-process of data and results included in Iber and GID are available online, for example, here:

:* [https://downloads.gidsimulation.com/GiD_Documentation/Courses/gid_basic/GiD_15_Basic_Courses.pdf https://downloads.gidsimulation.com/GiD_Documentation/Courses/gid_basic/GiD_15_Basic_Courses.pdf]
:* [https://www.gidsimulation.com/gid-for-science/whats-gid/postprocessing/ https://www.gidsimulation.com/gid-for-science/whats-gid/postprocessing/]
:* [http://www-opale.inrialpes.fr/Aerochina/info/en/html-version/gid_14.html http://www-opale.inrialpes.fr/Aerochina/info/en/html-version/gid_14.html]

Wood simulation´s results are also written in different text files (''.rep'') created during the computation inside the project folder. These files can be opened with a text editor.

''All .dat files are input files that are written when running the computation. The output files have a .rep extension. ''Details of these output files are described in the following section.

<span id='_Toc204064717'></span>
==5. Output files==

All output files are created inside the project folder in a folder named Wood (Fig.11).

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 
{|
|-
| [[Image:Draft_Ruiz-Villanueva_363145736-image14-c.png|126px]]
| [[Image:Draft_Ruiz-Villanueva_363145736-image15.png|center|102px|alt=''|]]
|}
</div>

'''Figure 11: Results folder named Wood and created result files'''

The first output file created when running Iber-Wood is the one named ''wood.rep''

This file shows all results from the wood transport simulation written for each time step and each log: Time (s); ilog; Name; X; Y; Angle; Length (m); Diameter (m); Vx,log (m/s); Vy,log (m/s); Vx (m/s); Vy (m/s); A_log; A_sub; Density (kg/m3); Manning; Depth (m); Elevation (m); Cd; Case; Travelled dist. (m); Straight dist. (m); Root_coef.

:* ''Ilog'' is the number of logs present in the simulation; this is not the number assigned to each log and changes with time
:* The ID of the log is the ''name'' of the log, which remains constant over time

The coordinates of the centre of mass are written together with the angle (in radians), its size (length and diameter in meters), log velocity (in the two directions, X and Y), the flow velocity of the element where the log´s centre of mass is located, the area of the log, the submerged area of the log (both in m<sup>2</sup>), the log´s density, the value of the manning roughness of the element where the log´s centre of mass is located, the water depth in meters and its elevation (m a.s.l.) of that element, and the log drag coefficient (Cd). Case refers to the state of the log (e.g., submerged, or emerged), but it is information for developers only. The actual and straight distances travelled by the log are also provided, and the root coefficient in the case of logs with roots.

At the end of the file a summary (Figure 12) is computed with the total number of supplied logs is together with the number of exited logs (outside the domain), logs deposited (only when log velocity=0 m/s) within the studied domain and number of moving logs within the domain (i.e., log velocity not equal to 0).

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image16.png|180px|alt='Figure 12: Summary of total number of supplied logs is together with the number of exited logs (outside the domain), logs deposited (only when log velocity=0 m/s) within the studied domain and number of moving logs within the domain (i.e., log velocity not equal to 0)'|Figure 12: Summary of total number of supplied logs is together with the number of exited logs (outside the domain), logs deposited (only when log velocity=0 m/s) within the studied domain and number of moving logs within the domain (i.e., log velocity not equal to 0)]] </div>

'''Figure 12: Summary of total number of supplied logs is together with the number of exited logs (outside the domain), logs deposited (only when log velocity=0 m/s) within the studied domain and number of moving logs within the domain (i.e., log velocity not equal to 0)'''

<span id='_Toc204064718'></span>
====Wood_gauges.rep====

This file (Fig. 13) contains the computation of a number of logs (cumulative) passing through the wood gauge (if created in the pre-process) at each time step.

<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">
 [[Image:Draft_Ruiz-Villanueva_363145736-image17-c.png|348px|alt=''''Figure 13: Wood_gauges.rep file''''|'''Figure 13: Wood_gauges.rep file''']] </div>

'''Figure 13: Wood_gauges.rep file'''

<span id='_Toc204064719'></span>
====WoodVol_gauges.rep====

This file is similar to the previous one, but instead of recording the number of logs, the volume of logs is written (in m<sup>3</sup>).

<span id='_Toc204064720'></span>
====Other output files====

''proceso.rep: ''This output file contains the information about the progress of the computation. It is the same information as shown in the View process info (Calculation Window).

<br/><span id="_Toc204064721"></span>
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