Tuesday, May 24, 2011

Carbonate pseudotachylytes: evidence for seismic faulting along carbonate faults

After a while I have a new paper accepted. Actually my role was very minor but I am proud of it, indeed.

From the abstract:
The Canalone Porta fault, developed within dolomitic and marly limestones in the Grigna Massif (Southern Alps, Italy), shows two types of reddish veins: one parallel to the principal slip plane (fault-veins) and the other intruding the fault host rock (injection- veins). The veins have a dominant carbonate composition and show a microtexture with millimetre-sized clasts embedded in a fine-grained matrix. This matrix is composed of micrometre-sized globular clusters of micrometre- to nanometre-sized calcite and dolomite crystals, bound together by K-bearing aluminosilicate glass. Field and petrological data suggest that this carbonate- rich matrix represents an undercooled melt-bearing assemblage produced at T 700 °C and P 0.1–0.2 GPa. The Canalone Porta veins are therefore carbonate pseudotachylytes, i.e. the friction-induced melting product of carbonate rocks. Herein, we discuss the scarcity of these rocks in general and criteria to find and recognize them along relatively deep fault zones.

The full paper can be found here

A second post on the JGrasstools in row

Please give a look to the announcement given by Andrea Antonello. There are at least two thing to notice: The Java wrapper to GRASS, and the presentation by Andrea which reveals the beauty of the concept of OMSBox. Please follow the link to read.

Tuesday, May 17, 2011

The first official release of the JGrasstools is out !

Searching for contributors, at the jgrasstools site thanks to the continuous and dedicated work of Andrea Antonello and Silvia Franceschi, the "Hydrologis".

Personally, I will confirm my commitment in increasing the science of their content, and to enlarge their scope. It's a major step forward the next JGrass, and to a new generation of GISs.

Friday, May 6, 2011

Programming and Doing Matrix Algebra in Java

Java is a great programming language. I really appreciate the enormous efforts that were made in making programmer life better, and the elegance of the Object Oriented programming, as compared to the procedural way of thinking I was used to.
Java is special for that being incredibly large the number of things that should be managed for its professional use. A possible workflow for learning it, is presented here (pay attentions to looping links).

At the very end  most of the core work I have to do, is to do linear algebra. Recently the Mathematical Libraries for Java grew many and interesting.   Information can be found in Wikipedia at the List of Numerical Libraries (but most of the links do not work, you have to google the names).

Among the libraries cited there, recently we used the Parallel Colt in the work by Francesco Serafin. The merit of the page Parallel Colt was also to bring my attention on the theory of what I was looking for, and especially to the CSparse book by Tim Davis, and to the Golub work, and book.

A comprehensive overview of Java Matrix Packages is given at the Java-Matrix.org.
A comparison of Matrix packages performance was made here but a test with our tools will be necessary, sooner or later.  UJMP is the only one of all the packages that also has a companion paper that tries to describe the design of the library. For me a great add-value.  Also la4j seems promising. Both la4j and UJMP seems to be currently updated, while other efforts are more or less quiescent (including Parallel Colt).

I also observe that a possible use of new features of Java 8 could be of some interest for matrix multiplication. However the most informed answers suggested to cope with ready-made work.

Before doing anything, remeber that for many problem Apache Commons, as well as the more specialised Math Commons and the Google Guava library already have a solution.

A lot to learn indeed.

Wednesday, May 4, 2011

OpenFOAM ... new basic libraries for GEOtop ?

Matteo Dall'Amico, of Mountain-eering brought to my attention the OpenFoam community at:


OpenFoam is a set of models and libraries for simulations of fluid dynamics problems. From their own site:

"The OpenFOAM® (Open Field Operation and Manipulation) CFD Toolbox is a free, open source CFD software package produced by a commercial company, OpenCFD Ltd. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
The core technology of OpenFOAM is a flexible set of efficient C++ modules. These are used to build a wealth of: solvers, to simulate specific problems in engineering mechanics; utilities, to perform pre- and post-processing tasks ranging from simple data manipulations to visualisation and mesh processing; libraries, to create toolboxes that are accessible to the solvers/utilities, such as libraries of physical models.
OpenFOAM is supplied with numerous pre-configured solvers, utilities and libraries and so can be used like any typical simulation package. However, it is open, not only in terms of source code, but also in its structure and hierarchical design, so that its solvers, utilities and libraries are fully extensible.
OpenFOAM uses finite volume numerics to solve systems of partial differential equations ascribed on any 3D unstructured mesh of polyhedral cells. The fluid flow solvers are developed within a robust, implicit, pressure-velocity, iterative solution framework, although alternative techniques are applied to other continuum mechanics solvers. Domain decomposition parallelism is fundamental to the design of OpenFOAM and integrated at a low level so that solvers can generally be developed without the need for any ’parallel-specific’ coding.
This section of the website describes some of the features of OpenFoam. The information is a little out of date, but more information will be added during 2010 to catalogue the full list of features of OpenFOAM. "

What could be important for us could be, not just the solvers, since we do solvers, but the tools and the rules. Soon in fact we will be facing to move our GEOtop C-based code to some object oriented language (possibly in a mmix of Java and C++). Object oriented programming has a lot of advantages with respect to procedural programming with respect to many topics, which can help us to do better programming and work more easily in cooperation. Since a full-Java solution could not be as efficient as we desire, using C++ could be the choice.

The lesson we learned from the past work is that large modelling efforts without a community supporting the various needs, is an overwhelming task. JGrass experience viceversa, taught us that one can learn a lot from a community of developers, even if they have slightly different scopes from ours, and even their presence help us.

Thus, OpenFoam, having a community, and having solved many of the problems we have with our own code, is a good candidate for substituting the old beloved Fluidturtle Libraries that I coded fifteen years ago

Monday, May 2, 2011

Deltares' Products become GPL !!!

From Edward Melger and Bert Jagers:

"If you're interested 2D/3D modeling of rivers, lakes, estuaries, coastal
and marine areas, join the Delft3D open source community at


Here we facilitate the Delft3D open source community to share knowledge,
brainstorm on new features and build working relationships. The source
code of the Delft3D modules FLOW + MOR + WAVE is available as free
software under GNU General Public License (GPL).

By going open source Deltares strives to enhance collaboration, combine
the unique expertise of researchers worldwide and further expand the
Delft3D modelling suite.

Deltares remains committed to supplying high quality services to
consultancy firms, governmental organizations, universities and research
institutes worldwide. See also Services on the webportal.

If you have any questions, please do not hesitate to contact us.

Best regards,

Edward Melger and Bert Jagers
Delft3D open source community website: http://oss.delft3d.nl"