Monday, December 30, 2013


Want to start with turbulence ? Start first with fluid dynamics:
  • George Batchelor [Old, but classics]
    • An Introduction to Fluid Dynamics ( I have the feeling to be able to do better in some parts - but without trying it how one can say ?)
Some freely available resources:

Regarding Turbulence itself, I would start from on-line resources, and the first reading could easily be:
which could continue continue with some selected topics by

If I have to choose just other three references, I would select (in brackets [ ] Shalizi's -see below-comments, in  ( ) my comments) :
  • George Batchelor [Old, but classics]
  • Uriel FrischTurbulence: The Legacy of A. N. Kolmogorov [An excellent introduction, very strong on defending Kolmogorov's work from misunderstandings and invalid criticisms.] One paper that summarizes Frisch view is here
and a different, but, in my opinion in the long-term the winning perspective:
Of the latter this paper by David Ruelle can be a complement.

Also the old classic book by Tennekes and Lumley  is available, legally or not, on-line, here.

Other stuff  which is intriguing me, are random cascades (and turbulence), a topic that I came to know through the work of Ed Waymire, and that you can come close by reading:
Also interesting is the works on rinormalization group and turbulences of which this is a google synthesis.

Finally, you can look at the Cosma Shalizi's bibliography. Huge and overwhelming indeed, it was the starting point of this my own post.

Sunday, December 29, 2013

Snowflakes (is Christmas time after all, and I live in a boreal place)

Christmas time remembered me to give a look to snow crystal formation literature and models. To my surprise, a definitive (thermodynamic) theory of their formation does not exist. This is what can be deduced form the review paper by the K.G. Libbrecht (2005).  Even if in two subsequent papers (2012 and 2013) he tries to delineate a possible path towards a comprehensive theory. Actually the attention to Libbrecht paper was brought to me by a paper on a three-dimensional model of snow-fakes (fakes ;-), not flakes) by Gravner and Griffeath. For a classification of snow crystal, Magono paper, would be fine. I am looking forward to read them all (starting from the Libbrecht review and his two most recent papers, which seem to add something) and complete this post more appropriately eventually. For the moment, be happy with the bibliography.

Some of the  references could look strange (e.g. Fu et al., 2006). In that case, I was looking for literature in the area of fractal surfaces. Something else should be available.  In particular, I was looking for a papers by J. Nittman and  Eugene Stanley (a "star" among the "fractalists"). In any case, growth of this type of forms is pretty general and ubiquitous (as shown in many papers, and in particular, in Ben Jacob's ones).

I also indulged in adding some papers about snow crystal methamorphism. This is not the topic of the post, but for the moment I keep trace of them in here. Other papers were just added for getting some general reference to crystal growth (e.g. the Krug's one, and those looking to micro-meteorological aspects of the growth).

Interesting readings are also addressed in this older post.


Ben Jacob, E. (1993). From snowflake formation to growth of bacterial colonies: Part I. Diffusive patterning in azoic systems. Contemporary Physics, 34(5), 247–273. doi:10.1080/00107519308222085

Ben-Jacob, E. (1997). From snowflake formation to growth of bacterial colonies II: Cooperative formation of complex colonial patterns. Contemporary Physics, 38(3), 205–241. doi:10.1080/001075197182405

Chen, J. P., & Lamb, D. (1994). Simulation of Cloud Microphisical and Chemical Processes using a Multicomponent Framework. Part I: Description of the Microphysical Model. Journal of the Atmospheric Sciences, 51(18), 2613–2630.

Chen, S., & Baker, I. (2010). Evolution of individual snowflakes during metamorphism. Journal of Geophysical Research, 115(D21), D21114. doi:10.1029/2010JD014132

Fu, F., Liu, L., Yang, K., & Wang, L. (2006). The structure of the self-organized blogosphere. arXiv:Physics, 1–5.

Fukuta, N., & Takahashi, T. (1999). The Growth of Atmospheric Ice Crystals: A Summary of Findings in Vertical Supercooled Cloud Tunnel Studies. Journal of the Atmospheric Sciences, 56(12), 1963–1979. doi:10.1175/1520-0469(1999)056<1963:TGOAIC>2.0.CO;2

Gravner, J., & Griffeath, D. (2007). Modeling snow crystal growth III: three dimensional  snow fakes. arXiv:Physics, 1–39.

Gravner, J., & Griffeath, D. (2009a). Modeling snow-crystal growth: A three-dimensional mesoscopic approach. Physical Review E, 79(1), 011601. doi:10.1103/PhysRevE.79.011601

Krug, J. (2002). Four Lectures on the Physics of Crystal GrowtharXivcond-Math, 1–43.

Libbrecht, K. G. (2005). The physics of snow crystals. Reports on Progress in Physics. doi:10.1088/0034-4885/68/4/R03
Libbrecht, K. G. (2013a). Aerodynamical Effects in Snow Cristal Growthth. arXiv:Physics, 1–23.

Libbrecht, K. G. (2013b). Toward a Comprehensive Model of Snow Crystal Growth Dynamics: 2. Structure Dependent Attachment Kinetics near -5 C. arXivcond-Math, 1–13.

Magono, C., & Lee, C. W. (1966). Meterological Classification of Natural Snow Crystals. Journal Of the Faculty of Sciences, Hokkaido University, Japan, 2(4), 312–345.

Nelson, J. (2005). Branch Growth and Sidebranching in Snow Crystals. Crystal Growth & Design, 5(4), 1509–1525. doi:10.1021/cg049685v

Nittmann, J., & Stanley, H. E. (1987). Non-deterministic approach to anisotropic growth patterns with continuously tunable morphology: the fractal properties of some real snowflakes. Journal of Physics a: Mathematical Genereral

Nelson, J., & Knight, C. (1998). Snow Crystal Habit Changes Explained by Layer Nucleation. Journal of the Atmospheric Sciences, 55(8), 1452–1465. doi:10.1175/1520-0469(1998)055<1452:schceb>;2

Rango, A., P, W. W., & Erbe, E. F. (1996). Snow crystal imaging using scanning electron microscopy: I. Precipitated snow. Hydrological Sciences–Journal–Des Sciences Hydrologiques, 41(2), 219–233.

Rango, A., P, W. W., & Erbe, E. F. (1996b), Snow crystal imaging using scanning  electron microscopy: II. Metamorphosed snowHydrological Sciences–Journal–Des Sciences Hydrologiques41(2), 235–250.

Reiter, C. A. (2005). A local cellular model for snow crystal growth. Chaos Solitons & Fractals, 23(4), 1111–1119. doi:10.1016/j.chaos.2004.06.071

Monday, December 16, 2013

USGS r-packages for hydrology

As I learn AGU Fall meeting, USGS is committed to develop various R Packages to help analysis of hydrological data.

These packages include:
  • GLRItcl
  • Splash page for USGS-R organization
  • EflowStats: Calculates Hydrologic Indicator stats and fundamental properties of daily streamflow for a given set of data
  • EGRET: An R-package for the analysis of long-term changes in water quality and streamflow, including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS)
  • EflowStats: Calculates Hydrologic Indicator stats and fundamental properties of daily streamflow for a given set of data. A related poster, presented at AGU Fall meeting 2013, can be found here.
  • USGSwsBase: Base USGS water science R functions.
  • surragateRegression
  • dataRetrieval: This R package is designed to obtain its water quality sample data, streamflow data, and metadata directly from either the USGS NWIS (National Water Information System), but it allows for user-supplied text files as inputs. The program is designed to ingest the data directly into R and structure them into file structures suited for EGRET analysis.
  • USGSwsQW: Water quality USGS water science R functions.
  • USGSwsStats:Statistic USGS water science R functions.
  • USGSwsData: Data sets as data.frames and as text files for examples in the USGS core pacakges
  • USGSwsGraphs: Graphical USGS water science R functions
  • restrend
  • rloadest
  • DVstats
  • NWCCompare
  • rGDP
  • functionCollection
All of them can be retrieved from the USGS-R Github repository. Link to other R packages useful for hydrology can be found at the main R post.

The Abouthydrology mailing list (at googlegroups)

Tired of keeping your own (and often outdated) list of colleagues to advertise your conference session, Ph.D. and postdoc positions, or other research opportunities?
Do you have a free software program or textbook of interest to the hydrologic community?
Wish you could just send one email and have it reach hundreds of your colleagues?

  Welcome to the About Hydrology mailing list! This acts the very same way the Gilbert Club list does for geomorphologists in being used to send announces about events, Ph.D. and post-doc positions, new books, open source software, AGU and EGU sessions and so on. All about hydrology, obviously.

The list has so far  (November 2020) almost 4000 active subscribers, and therefore sending around information through it is pretty effective, and save you the weight to maintain your own list of email addresses. 
To subscribe go to the page:!forum/abouthydrology  or Search “AboutHydrology Google Group”. Maintaners of the group are me, Stacey Archfield,  Giuseppe Formetta and Marialaura Bancheri.

Tuesday, December 10, 2013

GEOtop 2.0 at AGU 2013 - II - The Cryosphere

In this marathon I am doing at this Fall AGU Meeting, I am also giving a second talk about GEOtop 2.0. But this time I talk about the simulations of the snow modelling and the soil freezing.
The presentation is mainly based on the work initiated with Stefano Endrizzi and Matteo Dall'Amico thesis, and subsequently pursed together with Stephan Gruber of Zurich University, now at Carleton University. The two reference papers are Dall'Amico et al. 2011 and Endrizzi et al., 2013, cited in the talk, but also the work in Gubler et al. 2013 is extremely relevant for all the testing it performed on the models
So clicking on the image, as usual, you will gain access to the presentation. While, in the first post I took the occasion for adding the References of GEOtop, in this case I just collect the main presentations on the topic that you can find below.

GEOtop relevant presentation

Especially important to understand GEOtop history (see also these post: I and II).

GEOtop, the making of version 1.45  (Summer school on Environmental Dynamics, 2011)
summarised concepts already present in GEOtop 2008 presentation.

GEOtop, the snow modelling (now actually obsolete ... but a good reading for the general concepts)

Monday, December 9, 2013

GEOtop 2.0 at AGU 2013

I was invited to talk at a Fall AGU Meeting section about High Resolution Hydrological modelling. This is the topic of the H21M session of the meeting.  The following, below (clicking on) the figure is my interpretation of the topic.

I describe GEOtop 2.0, present a few case studies, and took the occasion to do some synthesis of this work. All the merits go to my co-authors, that in the last years strongly believed and pushed GEOtop beyond what it was. The presentation does not cover the cryospheric part of the models, which will be the focus of the second presentation.

This other posts covers my second presentation at AGU, talking about how the cryosphere is modeled in GEOtop 2.0.

GEOtop bibliography (so far)

Bertoldi, G., Rigon, R., & Over, T. M. (2006). Impact of Watershed Geomorphic Characteristics on the Energy and Water Budgets. Journal of Hydrometeorology,, 7, 389–403.

Bertoldi, G., Notarnicola, C., Leitinger, G., Endrizzi, S., Della Chiesa, S., Zebisch, M., & Tappeiner, U. (2010). Topographical and ecohydrological controls on land surface temperature in an Alpine catchment. Ecohydrology, 3(doi:10.1002/eco.129), 189–204.

Bertoldi G.; Della Chiesa, S; Notarnicola, C.; Pasolli, L.; Niedrist, G; Tappeiner, U. (2013), Estimation of soil moisture patterns in mountain grasslands by means of SAR RADARSAT 2 images and hydrological modeling, submitted to Journal of Hydrology

Bertoldi, G., Della, S., Notarnicola, C., Pasolli, L., Niedrist, G., & Tappeiner, U. (2014). Estimation of soil moisture patterns in mountain grasslands by means of SAR RADARSAT2 images and hydrological modeling. Journal of Hydrology, 516, 245–257.
Dall’Amico, M.; Endrizzi, S., Gruber, S; and Rigon, R. (2011), An energy-conserving model of freezing variably-saturated soil, The Cryosphere.

Della Chiesa, S.; Bertoldi, G.; Niedrist G., Obojes, N.; Albertson, J. D.; Wohlfahrt,G.; Hörtnagl L., Tappeiner U.,  (2014),  Modelling changes in grassland hydrological cycling along an elevational gradient in the Alps, Ecohydrol. 7, 1453–1473 (2014), DOI: 10.1002/eco.1471

Eccel, E., Cordano, E., & Zottele, F. (2015). A project for climatologic mapping of soil water content in Trentino. Italian Journal of Agrometeorology, 1(500 m), 5–20.
Endrizzi S. and Marsh P. Observations and modeling of turbulent fluxes during melt at the shrub-tundra transition zone 1: point scale variations, (2010) Hydrology Research

Endrizzi S., Gruber S., Investigating the effects of lateral water flow on spatial patterns of ground temperature, depth of thaw and ice content, Peer reviewed proceedings of the 10th International Conference on Permafrost, 25–29 June 2012, Salekhard, Russia, 91–96, 2012

Endrizzi S., Gruber S., Dall’Amico M., Rigon R., GEOtop 2.0. (2014), Simulating the combined energy and water balance at and below the land surface accounting for soil freezing, snow cover and terrain effects, 7(6), 2831–2857.

Fiddes, J., Endrizzi, S., & Gruber, S. (2015). Large-area land surface simulations in heterogeneous terrain driven by global data sets : application to mountain permafrost. The Cryosphere, 9, 411–426.

Fiddes, J., & Gruber, S. (2012). TopoSUB: a tool for efficient large area numerical modelling in complex topography at sub-grid scales. Geoscientific Model Development, 5(5), 1245–1257.

Formetta, G., Rigon R., David, O., Green, T. R., Capparelli, G. (2016), Integration of a spatial hydrological model (GEOtop) into the Object Modeling System (OMS), Water 8(1), 12

Gubler S., Endrizzi S., Gruber S., Purves R. S., Sensitivity and uncertainty of modeled ground temperatures and related variables in mountain environments, Geosci. Model Dev., 6, 1319–1336, 2013.

Gebremichael, M., Rigon, R., Bertoldi, G., & Over, T. M. (2009). On the scaling characteristics of observed and simulated spatial soil moisture fields, Nonlin. Processes Geophys., 16, 141–150.

Hingerl, L., Kunstmann, H., Wagner, S., Mauder, M., Bliefernicht, J., & Rigon, R. (2016). Spatio-temporal variability of water and energy fluxes - a case study for a mesoscale catchment in pre-alpine environment. Hydrological Processes.

Kunstmann, H.,  Hingerl, L., Mauder, M.,  Wagner, S., and Rigon, R., A combined water and energy flux observation and modelling study at the TERENO-preAlpine observatory, Climate and Land-surface Changes in Hydrology, Proceedings of H01, IAHS-IAPSO-IASPEI Assembly, Gothenburg, Sweden, July 2013 (IAHS Publ. 359, 2013)

Lewis, C., Albertson, J., Zi, T., Xu, X., & Kiely, G. (2013). How does afforestation affect the hydrology of a blanket peatland? A modelling study. Hydrological Processes, 27(25), 3577–3588.

Rigon, R., Bertoldi, G., & Over, T. M. (2006). GEOtop: A Distributed Hydrological Model with Coupled Water and Energy Budgets. Journal of Hydrometeorology, 7, 371–388.

Simoni, S., Zanotti, F., Bertoldi, G., & Rigon, R. (2007). Modelling the probability of occurrence of shallow landslides and channelized debris flows using GEOtop-FS. Hydrological Processes, doi: 10.10.

Zanotti, F., Endrizzi, S., Bertoldi, G., & Rigon, R. (2004). The GEOtop snow module. Hydrol. Proc., 18, 3667–3679. DOI:10.1002/hyp.5794.

Zi, T., Kumar, M., Kiely, G., Lewis, C., & Albertson, J. (2016). Simulating the spatio-temporal dynamics of soil erosion, deposition , and yield using a coupled sediment dynamics and 3D distributed hydrologic model. Environmental Modelling and Software, 83, 310–325.

Ph.D Thesis

Giacomo Bertoldi (2004) The water and energy balance at basin scale: a distributed modeling approachDownload PDF

Stefano Endrizzi (2009), Snow cover modelling at a local and distributed scale over complex terrain

Silvia Simoni (2009), A Comprehensive Approach to Landslide Triggering.

Matteo Dall'Amico (2011), Coupled Water and Heat Transfer in Permafrost Modeling.

Ageel Ibrahim Bushara (2011), Hydrological simulations at basin scale using distributed model and remote sensing with a focus of soil moisture.

GEOtop Manual

GEOtop Manual (a little out-of-date with respect to GEOtop 2.0 ... but not so much).

The Presentation at the Mountain Research Initiative Key Contact Workshop held in Berkeley Dec 8, 2013

After a few years, I am back to San Francisco AGU meeting. It is  a place where I grew up, since I participated ten times in 22 years.  For the very same reason that the fall meeting is crowded with more than twenty thousands of geophysicists coming from all around the World, many side meetings are organized. The MRI side meeting is one of these, and I participated.
The meeting involved a small group of people (around twenty) but was really interesting and productive. One can find all the contribution to discussion on the MRI website. At the moment, you can see my contribution by clicking on the image above. For knowing more about my research activities, these two posts can be useful: My past Research, Research Topics for the next 20 years.

Thursday, December 5, 2013

CUASHI ciber-seminars

For who do not, CUASHI stands for  Consortium of University for the Advancement of Hydrological sciences. The institution is a source of many good initiatives, among which, the hydrologic information system (HIS), a cyber-infrastructure for storing and distributing data.  However, one of the activity of CUASHI is covering with cyberseminars (more than one hundred so far) many aspects of hydrological research and practice.
Following the link you will findthe whole serie of seminar, in alphabetic order.  Out of them I chose ten, not necessarily the best, but those that have attracted my attention. All of them are the product of first class hydrologist, whose publication and studies deserve, in any case, attention. Here they are:

Bode, Collin - University of California, Berkeley
HydroWatch: An Open source Sensor Observatory
Recorded presentation

DeLuca, Cecelia - National Center for Atmospheric Research (NCAR)
ESMF and Earth System Curator: Integrated Modeling Infrastructure for Virtual Communities
Recorded presentation

Marks, Danny - USDA ARS, Northwest Watershed Research Center
An Outdoor Hydro-Climatic Laboratory for the 21st Century: 45 Years of Research and Data Collection at the Reynolds Creek Experimental Watershed
Recorded presentation

Molotch, Noah – Research at the Western Critical Zone Observatories
Snowmelt as a Driver of Ecohydrological Processes: Low-hanging Fruit for Cross-CZO Research
Recorded presentation

Pomeroy, John - University of Saskatchewan
Advancing Hydrological Processes to Better Predict Hydrology in Cold Regions
Recorded presentation

Selker, John - Oregon State University
Methods in Hydrologic Science: The Synergies between Redundant Low-cost Wireless Sensors and the Data Cloud Come of Age
Recorded presentation

Smith, Jim - Princeton University
Flooding in the Urban Environment
Recorded presentation

Tarboton, David & David R. Maidment - Utah State University & University of Texas, Austin
State and Regional Hydrologic Information Systems
Recorded presentation

Vogel, Richard - Tufts University
Hydromorphology: The Shape of our Water Future
Recorded presentation

Wagener, Thorsten - Pennsylvania State University
Hydrologic Similarity and the Search for a Catchment Classification Framework
Recorded presentation