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SOFTWARE

(revised 07/04/2013)

This is a list of links to computer software available on other servers.  URLs are given where you can download software at no cost.  Commercial software is not included.  The link for each software title leads to the home page (if available); follow the compute (Mac) (PC)  links for direct downloads.

mineralogic, crystallographic, spectroscopic

  • AMPH 2012 - gives the correct name to amphibole compositions after the IMA report (Hawthorne et al., 2012, American Mineralogist, 97, 2031-2048). This 2.0 version also covers orthorhombic amphiboles and acknowledges the recent recognition of the new rootnames ghoseite (for rootname 11) and suenoite (for the orthorhombic counterpart of rootname 3). Mistakes in the use of the magnesio- prefix have been corrected. Multiple entries from a file are now allowed. by Roberta Oberti.
  • CRUSH - calculates the Rigid Unit Mode spectrum for a given framework crystal structure. by Martin Dove.
  • DRAWxtl - displays crystal structures on ordinary computer hardware and operating systems. Four forms of graphics are produced: (1) an openGL window for immediate viewing, (2) the Persistence of Vision Ray Tracer (POV-RAY) scene language for publication-quality drawings, (3) the Virtual Reality Modeling Language (VRML) for dissemination across the Internet, and (4) a Postscript rendering of the OpenGL window for those that want high-quality output but do not have POV-RAY installed. DRAWxtl runs on Windows 2000, XP, Vista, Windows 7, and 8 (tested on the preview release), Mac (OS X), Linux, other Unix-type systems. and openVMS. No special graphics hardware is required.. by Larry W. Finger, Martin Kroeker, and Brian Toby.
  • EoSFit - to fit and manipulate equations of state, and other software for collecting and processing high-pressure single-crystal diffraction data. by Ross Angel.
  • GALOPER is a computer program (written in Microsoft Excel macro language) which simulates the shapes of crystal size distributions (CSDs) from the crystal growth mechanisms discussed in Eberl, D. D., Drits, V.A., and Srodon, J., 1998, Deducing crystal growth mechanisms for minerals from the shapes of crystal size distributions. American Journal of Science, v. 298, p. 499-533. Measured CSDs are simulated with Galoper to discover crystal growth history. It available for downloading from the USGS ftp site: GALOPER.  by Dennis D. Eberl.
  • GSAS-II (General Structure Analysis System) is is a complete crystallographic package in development that will run on Windows, Linux & MacOSX machines (developed on Windows so best there). It makes extensive use of computer graphics, both as a user interface and to display results.

    As of July 22, 2012, GSAS-II will read & process both x-ray and neutron (CW only) powder data in most any of the old GSAS file formats and single crystal data in IUCr CIF format. It can also read and process (e.g. calibrate & integrate) 2-D image powder data. Powder data processing includes peak fitting & indexing as well as Rietveld & Pawley refinement. Single crystal data can be used in combined or separate refinements as well. The system includes Fourier map preparation & display, peak picking and crystal structure display in a variety of forms (balls, balls & sticks, ellipsoids, polyhedra), as well as distance/angle/torsion/plane geometry results calculations with esds for the resultant data values. Constraint relations and equations may be applied upon parameters as needed. There is also a scheme for charge flipping structure solution for either single crystal or powder diffraction data (some further development is needed to complete this). More work is also planned to add facilities for restraints and rigid body refinement. Plans for handling neutron TOF data and analysis of magnetic/incommensurate/protein structures are in consideration.

    GSAS-II has been created by Robert B. Von Dreele and Brian H. Toby of Argonne National Laboratory. It is distributed via a subversion server at Argonne National Lab. and consists of python source code, some fortran source code (compiled for most platforms) and library modules, a suite of tutorials, and example data files. It requires python 2.7+ (but not python 3.+) and certain python packages (wxPython, numpy, scipy, matplotlib & pyOpenGL). Please see the wiki pages for full installation & operating instructions. To find the information use http://tinyurl.com/GSASII, or just Google "GSAS-II"; it probably will be the first thing listed. If you give GSAS-II a try, please let authors know your experiences and especially if you find bugs & errors. Suggestions are welcome. There is a also brand new GSAS-II mailing list, see http://www.aps.anl.gov/mailman/listinfo/GSAS-II; we request users sign up.

  • Isoplot from the Berkeley Geochronology Center is a flexible tool for the mathematical and graphical interpretation of radiogenic-isotope data, especially as applied to geochronology. Isoplot can: C
    • alculate and plot classical isochrons (Rb/Sr, Sm/Nd, U/Pb, Re/Os, Lu/Hf…);
    • Construct U-Pb concordia plots and calculate ages using conventional concordia intercepts, the “Concordia Age” algorithm, 3-D planar concordia intercepts, or 3-D linear (“Total U/Pb”) isochrons;
    • Calculate uranium-series isochron ages using 3-D or 2-D isochrons and construct 230Th/238U-234U/238U evolution curves and isochrons;
    • Plot Ar-Ar step-heating diagrams and find the statistically-best plateau steps and age;
    • Combine Ar-Ar isochron with Ar-Ar step-heating diagrams to obtain the logically optimum combination of both;
    • Use simple Bayesian constraints Improve the estimates and error-assignments for a package of stratigraphically-constrained radiometrically-dated units whose ages overlap within errors (with a special variant for 230Th/U ages);
    • Construct single-stage growth-curves for plots of com­mon-Pb data;
    • Construct cumulative-probability / histogram plots and linearized-probability diagrams;
    • Calculate both conventional (analytical-error weighted) and robust (nonparametric) x-y regressions for “classical” and Pb-Pb isochrons;
    • Deconvolute mixtures of components having Gaussian error-distributions using the Sambridge-Compston approach;
    • Calculate and construct plots for either error-weighted or robust (nonparametric) averages of a single variable;
    • Plot curves for almost any function;
    • Provide Monte Carlo errors as well as asymptotic (first-order) errors for most linear regressions, isochrons, and concordia-intercept solutions;
    • Extract reliable ages and errors from complex suites of Phanerozoic single-zircon dates;
    • Expand the number of Excel functions by more than 50, including many functions for radiogenic-isotopes (including 16 for U/Pb and 8 for 230Th-234U-238U alone).
    Isoplot is available without charge at http://www.bgc.org/isoplot_etc/isoplot.html.

  • KALI Jeff Weeks' Topology and Geometry Software. Play with the 17 plane groups, the 10 point groups (plus 5-fold symmetry) and even symmetry along a line geometrygames.org. Click on Kali, and download the appropriate version. Easy to use, just start it and click away.
  • MUDMASTER is a computer program (written in Microsoft Excel macro language) which determines mean crystallite size, crystallite size distribution and strain by Fourier analysis of X-ray diffraction peak shape. It is based on the Bertaut-Warren-Averbach technique, as has been described in Drits, V., Eberl, D. D., and Srodon, J., 1998, XRD measurement of mean thickness, thickness distribution and strain for illite and illite/smectite crystallites by the Bertaut-Warren-Averbach technique. Clays & Clay Minerals, v. 46, p. 38-50. The program is easy to use, and determinations are very accurate for nano-size crystals. It available for downloading from the USGS ftp site: MUDMASTER.  by Dennis D. Eberl.
  • NMRFIT - deduce the short-range Al/Si order in a framework aluminosilicate mineral from Si MAS-NMR data by means of a Monte-Carlo simulated anneal. by Martin Dove. 
  • WinPyrox - A Windows program for pyroxene calculation classification and thermobarometry (American Mineralogist, Volume 98, pages 1338–1359, 2013) by Fuat Yavuz. 
  • UnitCell : Program to refine unit cell parameters from powder diffraction data. by Tim Holland.  Mac PC
  • OccQP : Optimization of site-occupancies in minerals using quadratic programming, as described in the article by S.E. Wright, J.A. Foley, and J.M. Hughes (Am. Min., 2000). Written and maintained by Stephen E. Wright.
petrologic

  • ERUPT - graphical program that simulates various volcanic eruption types, including Strombolian, Plinian, Vulcanian/Surtseyan pyroclastic flows and surges, Hawaiian fluid lava flows, fumarolic activity, and Peléean viscous lava dome emplacement. Tectonic (faulting), caldera and sector collapse, and erosional events are also simulated. by Kenneth H. Wohletz.
  • Galoper - a program that simulates the shapes of crystal size distributions (CSDs) that result from a variety of crystal growth mechanisms, or from a combination of these mechanisms. Associated programs include statistical programs used for comparing calculated with measured CSDs, programs for calculating lognormal and gamma distributions, and a program for arranging crystal size measurement data into size groupings (bins). Available for downloading free of charge from a USGS ftp site: Galoper.
  • GCDkit - The GeoChemical Data ToolKIT is a system for handling and recalculation of whole-rock analyses from igneous rocks. It is written in R, a language and environment for statistical computing and graphics. Main features of GCDkit are:
    • Standard geochemical calculations involving major-, trace-element as well as Sr-Nd data
    • Effective data management (searching, grouping)
    • Common plots (binary, ternary, spider diagrams)
    • Graphic output to publication quality
    • Modular architecture (= easily expandable and modifiable)
    • Transparent functionality & availability (open source freeware, WWW)
    GCDkit version 2.3 was released on May 11, 2008. Currently, GCDkit works under the Windows GUI, and Windows XP/Vista/7 are recommended systems. Under previous versions of Windows R may become unstable, failing to redraw graphical windows if too many of them are open. Furthermore, our users reported GCDkit functionality under Linux with emulated Windows. by Janoušek, V., Farrow, C. M. & Erban, V. 2006. Interpretation of whole-rock geochemical data in igneous geochemistry: introducing Geochemical Data Toolkit (GCDkit). Journal of Petrology 47(6):1255-1259
  • GIBBS - generalized Jacobean transformation algorithm designed to perform thermodynamic calculations of heterogeneous phase equilibria useful to metamorphic petrology.  The program is designed to produce graphical output of results (phase diagrams, P-T diagrams, etc.) and there are several modules sesigned to facilitate different types of phase equilibrium calculations, plus the notes from a short course given at the NEGSA meeting in  Burlington, Vermont in March, 2001. by Frank Spear. MAC
  • GPT - Excel Spreadsheet for thermobarometric calculations in metapelitic rocks. by Reche & Martinez.
  • GTB - Macintosh GeoThermoBarometry program. by Matt Kohn and Frank Spear.
  • HandLens - program to calculate the major, minor and trace element chemistries and the isotopic compositions of individual minerals in mineral mixtures (e.g., in rocks, soils and sediments). The program inputs are the quantitative mineralogies (e.g., from RockJock analysis) and chemistries (e.g., from XRF or ICP-MS analyses) of bulk samples from related sample sets. The approach, which solves a series of simultaneous linear equations using Excel’s Solver tool, renders unnecessary the purification of mineral separates to determine individual mineral compositions. Available for downloading free of charge from a USGS ftp site: HandLens.
  • HEAT - 2-D, heterogeneous, heat flow simulator, useful for modeling magma chamber evolution. by Kenneth H. Wohletz.
  • Hbplag - Program to calculate temperatures for hornblende-plagioclase assemblages.  by Tim Holland.  Mac PC
  • MAGMA - Program to calculate the IUGG volcanic rock classification, CIPW norms, viscosity, and density of magmatic silicate liquids from chemical composition and temperature. by Kenneth H. Wohletz.
  • MELTS - a software package designed to facilitate thermodynamic modeling of phase equilibria in magmatic systems. It provides the ability to compute equilibrium phase relations for igneous systems over the temperature range 500-2000 °C and the pressure range 0-2 GPa. by Mark Ghiorso.
  • MudMaster - a program to calculate mean crystallite size, crystallite size distribution (CSD) and strain of nano-size minerals from Fourier analysis of XRD peak shape. MudMaster applies a modified version of the Bertaut-Warren-Averbach technique. The program was written to measure the thicknesses of clay crystals, but also has been applied, for example, to measure the CSDs of magnetic particles on computer disks, and the CSDs of metallic catalysts. The program works best for CSDs that have mean sizes <25 nm. Available for downloading free of charge from a USGS ftp site: MudMaster.
  • NICHOLS - gar-cor-sp-sil/ky-qtz thermobarometry (on-line calculations). by Geoff Nichols
  • OLIVERIAN - olivine thermobarometry. by Frank Spear. MAC
  • PERPLE_X - petrologic phase equilibria. by James Connolly
  • PhasePlot - a computational thermodynamics software package for visualizing equilibrium phase relations in application to the Earth and other silicate planetary bodies. The program determines abundances and compositions of solid and liquid phases based upon several thermodynamic data/model collections, including the work Ghiorso and colleagues (MELTS and pMELTS) on magmatic systems and the work of Stixrude and Lithgow-Bertelloni on phase relations in silicate systems at high pressure. The objective of PhasePlot is rapid visualization of equilibrium phase relations with the aim of promoting a deeper understanding of complex multicomponent systems and the utility of computational thermodynamics in broadening our appreciation of the natural world. The goal of PhasePlot is to create a computational environment that stimulates thinking about phase equilibria and its applications to natural systems, without the burden and distraction associated with the mechanics of performing these calculations. PhasePlot is a sophisticated calculator for the researcher and student of high-temperature phase equilibria. by Mark Ghiorso.
  • QUILF - PASCAL program to assess equilibria among Fe- Mg-Ti oxides, pyroxenes, olivine, and quartz. by Andersen, Lindsley and Davidson
    Mac
    UNIX
    DOS
  • RockJock - a free program for calculating the quantitative mineralogy from XRD patterns of randomly oriented powder samples. Analyses can be made with or without a corundum internal standard. The ideal, relative, 2-sigma error is ±4%. RockJock placed second in the most recent (2011) international Reynolds Cup quantitative mineral analysis competition. Available for downloading from the following USGS ftp site: RockJock. The program is almost entirely automatic, requiring only that the X-ray intensities for a sample be entered into the program, that minerals likely to be present be chosen from a list, and that a button be clicked. The instruction manual (RockMan) is available from the same site.  by Dennis D. Eberl.
  • SedUnMix - a free program for calculating the quantitative provenance of a mixed-source sediment from its quantitative mineralogy, and from knowledge of the quantitative mineralogy of source-area sediments. SedUnMix is described in Marine Geology 291-294 (2012) 24-33. Available for downloading free of charge from a USGS ftp site: SedUnMix.
  • SFT - graphical application designed to invert particle size data to find size distribution parameters of lognormal, sequential fragmentation, or sequential fragmentation/transport models, the latter two providing information about the fragmentation/transport origins of the sample (Wohletz et al., 1989, Jour Geophys Res 94: 15703-15721).  by Kenneth H. Wohletz.
  • StackMan - athat program calculates XRD patterns for mixed-layer illite/smectites from knowledge of the crystal thickness distributions of fundamental illite particles (e.g., using data from MudMaster analyses of illite crystal thicknesses determined from PVP-intercalated samples). The program is described in Am. Mineral. 96 (2011) 586-595. Available for downloading free of charge from a USGS ftp site: StackMan.
  • THERIAC-DOMINO - phase equilibria by free energy minimization. by Christian de Capitani. FORTRAN source codes .
  • Tetplot - plotting tetrahedral phase diagrams. by Frank Spear.
  • THERMOCALC - database for metamorphic phase equilibria. by Roger Powell and Tim Holland.
  • TWQ - thermodynamic database for metamorphic phase equilibria. by Rob Berman. 
  • UBC - retreivable mineral thermodynamic data. by Tom Brown.
  • WEBINVEQ - on-line thermobarometric calculations. by Terry Gordon.

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