Monday, March 31, 2025

Shima Azimi's Thesis and Presentation at graduation

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Sunday, March 30, 2025

A Ph.D. position ! Advanced Soil Biota-Hydraulics Interface for the WHETGEO-GEOSPACE system

Project Overview

This subproject, funded under the ICOSHELL project, aims to develop an integrated modeling
system that explicitly accounts for the dynamic interactions between soil biota activity and soil
hydraulic properties. Building upon the WHETGEO-1D and 2D frameworks, we will implement a
novel coupling between soil fauna population dynamics and plants root growth, evolving soil
hydraulic characteristics. The modelling system implemented will be eventually used for studying
the feedback between soil-vegetation hydrology.

Key Objectives

  • Extend the WHETGEO model architecture to incorporate time-varying soil hydraulic properties influenced by soil biota 
  • Implement the Kosugi soil water retention curve model with parameters that dynamically evolve based on biological activity
  • Develop and integrate a population dynamics module for key soil engineers (earthworms, ants, termites)
  • Create a comprehensive validation framework using laboratory and field experimental
  • data
Figure from Enrico Chiesa Master Thesis


Methodological Approach

The core innovation of this subproject is the implementation of a feedback loop between
 biological activity and soil physics. Following Meurer et al. (2020), we will start to model how earthworm populations modify soil structure, but significantly expand this approach by:

  • Replacing the van Genuchten model with the Kosugi water retention curve formulation, which provides a more direct physical interpretation of pore size distribution
  • Developing a differential equation system where the Kosugi parameters (median pore size and standard deviation) are directly modified by biological activity
  • Implementing these dynamics within the robust NCZ algorithm of WHETGEO, ensuring numerical stability across diverse conditions
  • The population dynamics will be modeled as a set of ordinary differential equations representing different functional groups of soil engineers, their reproduction, mortality, and activity rates as functions of environmental conditions (temperature, moisture, organic matter)

Expected Outcomes

This integration will allow to better capture:

• The temporal evolution of soil infiltration capacity following land-use changes

• The self-reinforcing positive feedback loops of ecosystem restoration, where initial

vegetation changes trigger soil biological activity that further enhances water retention

• The resilience of soil hydrological function under climate change scenarios


Implementation Timeline

Months 1-6: Preliminary studies, doctoral school activities

Months: 6-18 Implement Kosugi model in WHETGEO framework, develop and integrate

population dynamics module Months 18-24: Validate against experimental data Months 32-36:

Upscale to field applications and integration to estimate catchment scale effects. Study effects of

soil management

Possible collaborations

EPFL Lausannne, Prof. Sara Bonetti and Dr. Concetta D'Amato

Info: abouthydrology <at>  gmail.com
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Wednesday, March 12, 2025

The Marvelous Physics of Plants: a personal Introduction

 "The Marvelous Physics of Plants" presents an exploration of the physics behind how plants function, particularly focusing on water transport mechanisms. The presentation begins with poetic descriptions of plant processes, then explores Erwin Schrödinger's fundamental question about how physics and chemistry can explain the events within living organisms. The authors examine various physics domains relevant to plants: quantum physics, thermodynamics, hydraulics, micrometeorology, stability, and light.

Among the other things,  the authors examine the physical limits of tree height, discussing how hydraulic restrictions ultimately limit how tall trees can grow. They also demonstrate synthetic tree models that scientists have created to replicate these natural mechanisms.

The slides combine mathematical formulations, anatomical diagrams, and experimental results to illustrate the physical principles governing plant function. A video of the talk is also available.


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Friday, February 28, 2025

Three Batchelor Graduation Works

The first  Thesis-poster,  by Agnese Cavazzini, supervised by Gaia Roati and me, presents a hydrological study of the Secchia River basin using the GEOframe-NewAGE system. The research analyzes water balance and simulates river flow while generating soil moisture maps to identify drought-prone areas. Key elements include watershed division into sub-basins, mass balance equations, and calibration against measured data. Results show flow simulations at two monitoring stations and soil moisture anomaly maps. The successful implementation provides valuable insights into the basin's hydrological dynamics across Modena, Reggio Emilia, and Mantova provinces. You can get a high resolution poster by clicking on the Figure below..


The second Thesis-poster, by Lorenzo Dalsasso,  presents a statistical analysis of ground precipitation patterns by Lorenzo Dalsasso. Using hourly precipitation data from three weather stations, the study evaluates which probability distributions best represent precipitation duration, intensity, and intervals between events. A Python notebook with Kolmogorov-Smirnov tests determined that lognormal distributions best fit precipitation durations, Weibull distributions best represent precipitation intensities, and either Weibull (stations ID 40 and 1100) or lognormal (station ID 263) best characterize intervals between precipitation events. The results include detailed statistical parameters for each station. The high resolution poster can be found by clicking on the Figure below. 




Thr third thesis-poster presents Marco Feltrin's study on evapotranspirative fluxes in grapevines by integrating the GEOSPACE ecohydrological model with WiseConn sensor technology (dr. Marco Bezzi). The research compares two rainfall scenarios: a wet scenario (1147 mm of total precipitation) and a dry scenario (682.4 mm of total precipitation) to evaluate plant water stress. Using the one-dimensional GEOSPACE model with data from a vineyard near Verona, results show that the dry scenario led to half the plant transpiration during summer months. The model effectively demonstrates how water content throughout the soil column affects water stress in plants, with practical applications for irrigation management, water conservation, and predicting water availability for viticulture under changing climate conditions.  The high resoltion poster can be found by clicking on the Figure below. 







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Thursday, February 6, 2025

Biosphere, Atmosphere, Climate Interactions 2025 Class


The second part of this course explores the Soil-Plant-Atmosphere Continuum (SPAC). Below you will find materials covering soil properties, their mathematical representations, and an introduction to plant functioning. Students are expected to review these materials as an assignment before our class discussion of the concepts. In the latter portion of the course, we will conduct numerical experiments together using the GEOSPACE system.


Radiation

Water in soils 
 (Storyboard2020)
Once precipitations arrive to the ground surface they either infiltrate or generate runoff. We first state how they infiltrate and, actually how water behave in the soil and in the ground. We talk about the complexity of the Earth surface that contains life and call it, the Critical Zone. To study infiltration we introduce the Darcy and Richards equations of which we explain the characteristics.
  • A deeper view on matric potential 

Evaporation generalities (Storyboard2020)

A consistent part of root zone and surface water evaporates and returns to the atmosphere to eventually form clouds and precipitation again. The process follows quite complicate routes and is different when happening from liquid surfaces, soil or vegetation (and BTW animals).  In this group of lectures we try to figure out the physical mechanisms that act in the process and give some hint on methods to estimate evaporation and transpiration with physically based models. 
  • Supplemental Material
A little on the carbon cycle

The carbon cycle is intrinsically and fundamentally intertwined with both hydrological and climate cycles, forming an interconnected web of Earth system processes that operate across multiple temporal and spatial scales. While carbon dynamics were historically studied as a separate discipline from hydrology and meteorology, this artificial separation has dissolved as hydrology and meteorology have evolved into a comprehensive Earth System Science that recognizes the profound interconnectedness of all planetary processes. The integration of carbon cycle studies with hydrology represents a paradigm shift in our understanding of how Earth's systems function. Water serves as the primary medium through which carbon moves between the atmosphere, biosphere, hydrosphere, and geosphere, while carbon dynamics simultaneously influence water availability, quality, and distribution patterns. This bidirectional relationship creates a complex network of feedbacks that are not merely numerous, but virtually countless in their manifestations and interactions.


Further Reading

D’Amato, Concetta, and Riccardo Rigon. 2025. “Elementary Mathematics Can Help to Shed Light on the Transpiration Budget under Water Stress,” January. https://doi.org/10.1002/ECO70009.


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The Hydrological Modeling 2025 class

 Welcome to the 2025 Hydrological Modeling Class!

To better understand the materials provided:

  • Storyboards – Summaries of the lectures, usually in Italian.
  • Whiteboards – Explanations of specific topics, presented on a whiteboard using Notability on an iPad.
  • Slides – Commented in English (available since 2021).
  • Videos – Recorded during lectures to complement the slides, with no editing (as post-production would be too time-consuming).
    • 2025 videos are available on a [Vimeo Showcase] (link here).
  • Additional information & references – Marked in italics, for the curious and the brave who want to explore further.

📅 24 February 2025 – Part I

Syllabus & Introduction to Hydrological Modeling

In this session, I introduced the course and its learning-by-doing philosophy. We cover all theoretical concepts first, followed by the practical applications (with Professor Giuseppe Formetta).

The real start 

To begin is also worth to have a little (philosophical) analysis of what a model is. This is what done in the following parte of the lecture

📅 25 February 2025 – Geomorphometry

This session begins with a discussion of previous lesson topics and the rationale behind introducing geomorphometric concepts. Since catchments are spatially extended, understanding their geometry is essential for studying catchment hydrology.

In the first part, we focus on the geometrical and differential characteristics of topography, including:

  • Elevation
  • Slope
  • Curvature

These parameters are fundamental for extracting the river network and identifying different parts of a catchment.

We then define drainage directions and explore how they are computed using Digital Elevation Models (DEMs)—where topography is discretized on a regular grid. From these drainage directions, we determine the total contributing area at each point of a DEM.

These two key characteristics allow us to:

  1. Identify channel heads and extract the river network.
  2. Define hillslopes and establish an initial framework for Hydrologic Response Units (HRUs).

    📅 3 March 2025 

    Q&A - 

    Interpolations 
    This lecture, assuming that now you have at least the concepts of what a catchment is and theoretically you know how to extract it and subdivide it in parts, deals with the data to feed catchments hydrology models. Because catchments have a spatial distribution, then also the driving data must be distributed. We need therefore methods of interpolation. 

    Installations of the software can be found here, at this link.

    📅 10 March 2025 

     Interpolations part II
    In this class we try to understand how to estimate the errors over the estimates. Besides we introduce a method (the Normal Score) to avoid to obtain negative values when positive interpolated values are required.
    Q&A - 
    Spatial Interpolation (Vimeo2023)

    Hydrological Models. This is a class about hydrological models, so what are they ?

    The title is self-explanatory. A theoretical approach to modelling is necessary because we have to frame properly our action when we jump from the laws of physics to the laws of  hydrology. Making hydrology we do not have to forget physics but for getting usable models we have to do appropriate simplifications and distorsions. The type of model we will use in the course are those in the tradition are called lumped models. Here we also introduce a graphical tool to represent these models.

    📅 17 March 2025 

    Hydrological Models 

    For old material give a look to Hydrological Modelling 2023

    📅 25 March 2025 

     Linear Models for HRUs

    Once we have grasped the main general (and generic) ideas, we try to draw the simplest systems. They turn out to be analytically solvable, and we derive their solutions carefully. From the group of linear systems springs out the Nash model, whose derivation is performed.  Obviously, it remains the problem to understand how much the models can describe "reality". However, this an issue we leave for future investigations.
    A little more on the IUH and looking at the variety of HDSys models

    We introduced previously without very much digging into it the concept of Instantaneous Unit Hydrograph. Here we explain more deeply its properties, Then we observe that there are issues related to the partition of fluxes and we discuss some simple models for obtaining them. Not rocket science here. The concept that we need those tools is more important than the tools themselves. We also observe that linearity is not satisfactory and we give a reference to many non linear models. Finally we discuss an implementation of some of the discussed concepts in the System GEOframe. 

    📅 31 March 2025 

      📅 7 April 2025 

      • Additional material
      Digressions I - A Glimpse on distributed process-based models
       Travel Time, Residence Time and Response Time
      Here below we started a little series of lectures about a statistical way of seeing water movements in catchments. This view has a long history but recently had a closure with the work of Rinaldo, Botter and coworkers. Here it is presented an alternative vie to their concepts. Some passages could be of some difficulty but the gain in understanding the processes of fluxes formation at catchment scale is, in my view, of great value and deserves some effort.  The way of thinking is the following: a) the overall catchments fluxes are the sum of the movements of many small water volumes (molecules); b) the water of molecules can be seen through 3 distributions: the travel time distribution, the residence time distribution and the response time distributions; c) the relationships between these distributions are revealed; d) the relation of these distributions with the the treatment of the catchments made through ordinary differential equations is obtained through the definition of age ranked distributions; e) The theory this developed is a generalizations of the unit hydrograph theory. 

      📅 14 April 2025 

      Some References (advanced)
      Additional material

      Digressions I - A Glimpse on distributed process-based models
      Digressions II - Radiation -  After all radiation moves it all.
      Digressions III 
      Equations for disease spreading (Out of schedule)
      Digressions IV

    • Examples of Applications:
      • Intermedia
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          Tuesday, February 4, 2025

          The Hydrology Class Lab 2025

           The lab component makes up nearly half of the course, following the motto:

          "Learning by doing."

          Throughout the lab, you will conduct at least three key numerical experiments:

          • Time Series Analysis – Exploring various data elaborations with various Jupyter Notebooks and a little of Python
          • Intensity-Duration-Frequency (IDF) Curves – Estimating rainfall intensity over different time scales with various Jupyter Notebooks and a little of Python, as well 
          • Infiltration Experiments – Investigating soil absorption dynamics using the WHETGEO system
          • Evaporation & Transpiration Experiments – Understanding water loss processes in different conditions using the GEOSPACE ssytem

          Resources

          🔹[Vimeo Showcase – General Lab Videos]

          🔹[OSF Repository – Lab Materials]

          🔹[Theory and Concepts here]

          📌 Detailed videos and materials for each experiment are listed below.



           2025-03-03 Introduction to working with Jupyter and Notebooks

          2025-03-10 How to read and plot data
          2025-03-25 San Martino Reprise
          2025-03-31 Gumbel derivation

          Interpolating the Gumbel distribution to annual precipitation maxima
          2025-04-08 Where to find the data
          • Finding the data for the Time Series Analysis (Vimeo2025)
          2025-05-05 - Installations
          • Installing the GEOframe_vincennes environment
          • Installing the Java Development toolkit V11
          2025-05-06  

          Below, you'll discover the resources for the second part of the lab, which encompass instructions for utilizing Object Modelling System version 3 (OMS3) models such as WHETGEO1D and GEOET. Within the OMS Projects, you'll find a directory named Jupyter_Notebook, housing sets of notebooks designed to guide you through handling both input and output data for these programs.

          A general introduction to some OMS3 concepts
          2025-05-11
           Introduction to Infiltration with WHETGEO 1D. WHETGEO specifically focuses on simulating the coupled processes of water and heat transport, which are crucial for understanding: Soil moisture dynamics, Evapotranspiration processes, Energy balance at the land surface, Groundwater-surface water interactions, Snow and ice processes (where temperature is critical)
          2025-06-03

              Radiation estimation is preliminary to any Evapotranspiration estimation since our models use it as input. The estimation of radiation, as it results from the theory, needs a few GIS operations to determine the sky view factor and the aspect of the terrain in the point of interest. These operation for the present exercise are skipped and pre-analyzed data are provided. 
          • Please see the 05_NET.sim file in the project's simulation folder (Vimeo2025)
          • Inputs are in Input_Radiation.ipynb (Vimeo2025)
          • Outputs are in the Output_Radiation.ipynb (Vimeo2025)
          • The simulation runner is Runner_NetRadiation.ipynb (Vimeo2025)
           
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