Scientific Software

This program is intended to make working with the Generic Mapping Tools (GMT) easier. iGMT provides a graphical user interface for GMT and is written in the Tcl/Tk computer language. Besides supplying a user friendly way of handling GMT, iGMT comes with built-in support for many different geoscientific data sets, such as topography, gravity, seafloor age, hypocenter catalogs, plate boundary files, hotspot lists, CMT solutions etc.

This site aims at helping you identify ready to use solutions for your optimization problem, or at least to find some way to build such a solution using work done by others. Where possible, public domain software is listed here. This guide was started and maintained jointly for several years with Peter Spellucci, TU Darmstadt. It is now maintained by H.D. Mittelmann at the School of Mathematical and Statistical Sciences at Arizona State University.

The NVIDIA SDK provides high-performance tools and libraries to power innovative GPU-accelerated applications in machine learning, artificial intelligence, deep learning, virtual reality, visualization, and more.

PyFlux is a library for time series analysis and prediction. Users can choose from a flexible range of modelling and inference options, and use the output for forecasting and retrospection. Users can build a full probabilistic model where the data y and latent variables (parameters) z are treated as random variables through a joint probability p(y,z). The advantage of a probabilistic approach is that it gives a more complete picture of uncertainty, which is important for time series tasks such as forecasting. Alternatively, for speed, users can simply use Maximum Likelihood estimation for speed within the same unified API.

Instaseis calculates broadband seismograms from Green’s function databases generated with AxiSEM and allows for near instantaneous (on the order of milliseconds) extraction of seismograms. Using the 2.5D axisymmetric spectral element method, the generation of these databases, based on reciprocity of the Green’s functions, is very efficient and is approximately half as expensive as a single AxiSEM forward run. Thus this enables the computation of full databases at half the cost of the computation of seismograms for a single source in the previous scheme and hence allows to compute databases at the highest frequencies globally observed. By storing the basis coefficients of the numerical scheme (Lagrange polynomials), the Green’s functions are 4th order accurate in space and the spatial discretization respects discontinuities in the velocity model exactly. In addition, AxiSEM allows to include 2D structure in the source receiver plane and readily includes other planets such as Mars.

LASIF (LArge-scale Seismic Inversion Framework) is a data-driven end-to-end workflow tool to perform adjoint full seismic waveform inversions. Dealing with the large amounts of data present in modern full seismic waveform inversions in an organized, reproducible and shareable way continues to be a major difficulty potentially even hindering actual research. LASIF improves the speed, reliability, and ease with which such inversion can be carried out.

This project focuses on the use of the seismic ambient noise to monitor slight changes of properties in the solid Earth. The implications are the detection of change of strain at depth with applications in different contexts. A major field of application is the monitoring of potentially dangerous structures like volcanoes or active fault zones. The project includes new methodological developments, massive processing of existing data and field experiments. Applications in regions where changes are induced by human activity are important both for the quantitative refinement of the method and for the important economic and social implications of these problems.

This a collection of tools to run HypoDD by Felix Waldhauser. It takes event files in the QuakeML format, station data in the SEED format and waveform data in any format ObsPy can read and does all the rest. The output is one QuakeML file with the relocated events having one additional Origin node. The events that could not be relocated will not be changed.

ObsPy is an open-source project dedicated to provide a Python framework for processing seismological data. It provides parsers for common file formats, clients to access data centers and seismological signal processing routines which allow the manipulation of seismological time series.

The goal of the ObsPy project is to facilitate rapid application development for seismology.

These programs focus on the understanding and interpretation of seismic wave propagation in the crust and upper mantle of the Earth. Synthetic seismograph code is provided for sources and receivers at arbitrary positions in the plane layered media. Programs are provided for determination of crustal structure through the inversion of surface-wave dispersion and teleseismic P-wave receiver functions. Inversion of broadband recordings of regional earthquakes for source depth, focal mechanism and seismic moment is also provided. Finally, a new tool, gsac, is provided to permit interactive and script based manipulation of seismic traces. The entire package is well integrated in that the same Earth velocity model, waveform and graphics formats are used by all programs. A complete interactive graphics package is also provided.

OpendTect software consists of an open source part and an (optional) closed source part. The open source (base) part originates with dGB Earth Sciences, who act as custodians of the system and take care of: new developments, testing, releasing and support. As with all open source software systems, anyone can contribute to bring this software to a higher level. The closed source part of OpendTect consists of commercial plugins.

SEGTeX is a LaTeX package for geophysical publications. It consists of
- LaTeX2e class files for Geophysics papers, SEG expanded abstracts, etc
- BibTeX style files seg.bst
- BibTeX cumulative bibliography of geophysical publications SEG.bib
- latex2html customizations.

Madagascar is an open-source software package for multidimensional data analysis and reproducible computational experiments. Its mission is to provide a convenient and powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields.

CliFlo is a web portal to the New Zealand National Climate Database and provides public access (via subscription) to around 6,500 various climate stations (see <http://cliflo.niwa.co.nz/> for more information). Collating and manipulating data from CliFlo (hence clifro) and importing into R for further analysis, exploration and visualisation is now straightforward and coherent. The user is required to have an internet connection, and a current CliFlo subscription (free) if data from stations, other than the public Reefton electronic weather station, is sought.

R is ‘GNU S’, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. CRAN is a network of ftp and web servers around the world that store identical, up-to-date, versions of code and documentation for R.

Export your network from Gephi to a predefined Sigma.js template. Choose to include search, group selection, explanatory text, etc. without having to do any HTML/JavaScript coding. Upload the output to any webserver and enjoy a rich HTML5 interactive visualization of your network.

Gephi is the leading visualization and exploration software for all kinds of graphs and networks. Gephi is open-source and free.
Runs on Windows, Mac OS X and Linux.

The MDTools suite is a collection of programs, scripts, and utilities we provide for researchers to make various modeling and simulation tasks easier, and to provide basic code and utilities which can be built up into larger toolsets. Each tool, script, or library is listed below and has its own separate distribution, documentation, etc. The programs in this collection are provided for the benefit of the research community, but are not officially supported unless otherwise stated. Each program may have a software license and/or citation suggestions which should be listed on its web page.

NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.