Department of Geosciences
North Dakota State University
Software
List
Rainer Petschick's awesome software compilation, including excel spreadsheet macros.
The Dept. of Geosciences in Erlangan has programs for X-ray mineralogy and sediment settling
The Department of Earth Sciences at Cambridge University has programs for X-ray mineralogy and thermodynamic calculations
The UK Earth Science Courseware Consortium
at http://info.mcc.ac.uk/Geology/CAL/index.html
(Anonymous ftp: ftp.mcc.ac.uk/pub/geology)
contains a wide variety of teaching software.
Email address: ukescc@man.ac.uk
http://rsb.info.nih.gov/nih-image/
NIH Image is a public domain image processing and analysis program for the Macintosh. It was developed at the Research Services Branch (RSB) of the National Institute of Mental Health (NIMH), part of the National Institutes of Health (NIH).
A free PC version of Image, called Scion Image for Windows, is available from Scion Corporation. There is also Image/J, a Java program inspired by Image that "runs anywhere".
Image can acquire, display, edit, enhance, analyze and animate images. It reads and writes TIFF, PICT, PICS and MacPaint files, providing compatibility with many other applications, including programs for scanning, processing, editing, publishing and analyzing images. It supports many standard image processing functions, including contrast enhancement, density profiling, smoothing, sharpening, edge detection, median filtering, and spatial convolution with user defined kernels.
Image can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles. Spatial calibration is supported to provide real world area and length measurements. Density calibration can be done against radiation or optical density standards using user specified units. Results can be printed, exported to text files, or copied to the Clipboard.
A tool palette supports editing of color and gray scale images, including the ability to draw lines, rectangles and text. It can flip, rotate, invert and scale selections. It supports multiple windows and 8 levels of magnification. All editing, filtering, and measurement functions operate at any level of magnification and are undoable.
Image directly supports Data Translation and Scion frame grabber cards for capturing images or movie sequences using a TV camera. Acquired images can be shading corrected and frame averaged. Other frame grabbers are supported via plug-in modules.
Image can be customized in three ways: via a built-in Pascal-like macro language, via externally compiled plug-in modules and on the Pascal source code level.
Example macros, plug-ins and complete source code can be downloaded from the Download page.
More information about NIH Image can be found in the Overview section of the manual.
System Requirements
Image requires a color capable Macintosh and at least 4MB of free RAM. 32MB or more of RAM is recommended for working with 3D images, 24-bit color or
animation sequences. System 7.0 or later is required. Image directly supports, or is compatible with, large monitors, flatbed scanners, film recorders, graphics tablets, PostScript laser printers, photo typesetters and color printer
http://cires.colorado.edu/people/jones.craig/CHJ_PMag_overview.html
Craig H. Jones, cjones@mantle.colorado.edu
MicroWorld requires system 6.07 or higher, a 68020 processor or higher and the presence of Color QuickDraw.
Here is the complete URL for the Cornell anonymous FTP server where you can download a Stereonet program as well as other structure programs for the Mac by Rick Allmendinger. Please remember that this software is free to NON-commercial users only.
You will need to use the complete address to download the files from this site.
ftp://www.geo.cornell.edu/pub/rwa/
Rick Allmendinger
Dept. of Geological Sciences
3128 Snee Hall
Cornell University, Ithaca, NY 14853-1504
Tel. (607) 255-3376, FAX (607) 254-4780
e-mail: rwa1@cornell.edu or allmendin@geology.cornell.edu
Below are the other programs at this site:
Version 4.9 includes three significant new additions:
You now have more control over the appearance of the fonts (i.e. type, style, and size) that appear in the Plot window with the Fonts etc. command under the Symbols menu.
You can now annotate the plot window directly with the Annotate Plot command in the Symbols Menu. Choose this command, click on the spot in the window where you want the left edge of the text to start, and type. Entry is terminated with a RETURN, so you can only enter one line of text (256 characters, max). The font and style are controled by the Fonts etc. dialog box.
Stereonet now supports printing to any printer from within the program. You can print just the Plot Window or both the Plot and the Record windows together. Note that I had to change around some menu commands to fit with Mac interface guidelines: comma nd-P now prints the Plot window (cmd-P used to save the plot to disk); command-S now saves the plot to disk (cmd-S used to save a text file of the data); and command-D now saves the data to disk as a text file (cmd-D used to give you the current d ata count, which now has no menu command).
P-T-t computer programs from Frank Spear
These are programs were originally distributed at AGU and GSA short courses on metamorphic P-T paths. Dr. Spear has published a book on metamorphic phase equilibria and several computer programs to perform calculations of interest to metamorphic petrologi
sts.
Frank Spear
spear@harold.geo.rpi.edu
See:
Spear, F.S. and Peacock, S.M. (1989) Metamorphic Pressure-Temperature-Time Paths, 102 p. American Geophysical Union,Washington.
or:
Spear, F.S. (1993) Metamorphic Phase Equilibria and Pressure-Temperature-Time Paths, 799 p.
Mineralogical Society of America, Washington, D. C."
General Description of Program Thermobarometry
The purpose of program Thermobarometry is to perform and plot the results of thermobarometry calculations. The program was written by Matthew J. Kohn at Rensselaer Polytechnic Institute (now at U. Wisconsin) and has been modified for the Macintosh by F. Spear. An attempt has been made to incorporate all reasonable calibrations of thermobarometers for crustal rocks that have been published in the literature. New code is being added frequently.
This program manual contains description of computer programs and exercises on how to run the programs. The theoretical background is discussed at length in a set of short course notes published by the American Geophysical Union and distributed at 28th I nternational Geological Congress, which was held in Washington, D.C. in July, 1989 (Spear, F.S. and Peacock, S.M. (1989) Metamorphic Pressure-Temperature-Time Paths, 102 p. American Geophysical Union, Washington.) and is also discussed in Spear, F.S. (199 3) Metamorphic Phase Equilibria and Pressure-Temperature-Time Paths, 799 p. Mineralogical Society of America, Washington, D. C.) among other places.
Frank Spear; spear@harold.geo.rpi.edu
Hornblende-plagioclase geothermometry
hbplag is a public domain application for calculating hornblende-plagioclase geothermometry on the Macintosh. It is based on the thermometers of Holland and Blundy (1994, Contrib. Mineral. Petrol., v. 116).
Also see the link at the Department of Earth Sciences at Cambridge University, which has programs for X-ray mineralogy and thermodynamic calculations.
Tim Holland
Dept. of Earth Sciences
Cambridge CB2 3EQ
UK
PHREEQC is a computer program written in the C programming language that is designed to perform a wide variety of aqueous geochemical calculations. PHREEQC is based on an ion-association aqueous model and has capabilities for (1) speciation and saturation-index calculations; (2) reaction-path and advective-transport calculations involving specified irreversible reactions, mixing of solutions, mineral and gas equilibria, surface-complexation reactions, and ion-exchange reactions; and (3) inverse modeling, which finds sets of mineral and gas mole transfers that account for composition differences between waters, within specified compositional uncertainties.
Available from http://h2o.usgs.gov/software/phreeqc.html.
Point of contact for PHREEQC:
U.S. Geological Survey
Hydrologic Analysis Software Support Team
R. Steven Regan
437 National Center
Reston, VA 20192
(electronic mail: h2osoft@usgs.gov)
For a version of PHREEQC that you can run directly from your web browser, check out Web-Phreeq!
Crystal 2.29 is a public domain application for stererographic projection (crystallography) on the Macintosh, written and compiled in Microsoft Quickbasic.
It draws projections for any crystal system, with great circles as desired. It has a number of utilities, including one which can be used to solve back-reflection Laue patterns. It was developed for use in a Cullity-based X-ray course, and was marketed as a "commercial" product for a few years.
Crystal 2.29 runs on Mac II series, and MAY still run on earlier smaller Macs.
It runs with System 6.0.7 and 7.0.
CrystalView 1.0 is a public domain application for drawing and manipulating crystal unit cells on the Macintosh. It runs on Mac II series, and MAY still run on earlier smaller Macs. It runs with <>System 6.0.7 and 7.0.
"CrystalView 1.0 is a unit cell drawing Mac application written and compiled in Microsoft Quickbasic. It was written as an educational tool. One enters the crystal coordinates, screen dimension and color of each atom i n the basis group, and defines the unit cell shape and centering (primitive, body-, base- or face-centering) independently of basis group. The cell can be viewed in orthonormal projection from any direction by moving the mouse around in a stereo projecti on circle, or by typing in indices. Drawings can be printed, or copied to the clipboard.
Since this was written as an educational tool, there is a facility for hiding any desired atoms of the basis group so one can view the configuration of a subset of atoms, say the oxygens in spinel or interior atoms in GaAs. One can attach a tetrahedron t o a group of atoms, but I have never finished a more complete facility for adding other construction lines."
Thomas H. Kosel
Dept. Electrical Engineering
University of Notre Dame
Notre Dame, IN 46556
(219) 631-5642
Thomas.H.Kosel.1@nd.edu
March 25, 1994
RasMol 2.5 Molecular Graphics Visualisation tool.
Roger Sayle
BioMolecular Structures Group
Glaxo Research & Development
Greenford, Middlesex, UK.
October 1994
This posting is to announce the release of RasMol version 2.5. This latest version is available for the Apple Machintosh and PowerMac in addition to UNIX, VMS and Microsoft Windows versions. RasMol is a molecular graphics program intended for the visu
alisation of proteins, nucleic acids and small molecules. The source code is public domain and freely distributable provided that the original author is suitably acknowledged. The complete source code and user documentation may be obtained by anonymous FT
P from ftp.dcs.ed.ac.uk
[129.215.160.5] in the directory /pub/rasmol.
The source code, documentation and Microsoft Windows executables are stored in several files appropriate for the receiving operating system. Please read the "README" file in the distribution directory. UNIX and VAX systems should retreive either RasMol2.tar.Z, RasMol2.tar.gz. Apple Mac users should retrieve rasmac.sit.hqx.
Microsoft Windows users should retrieve raswin.zip and optionally the Visual Basic package rasmenu.zip. All these files include source code, on-line help, user manual and reference card. RasMac.sit.hqx, RasWin.zip and RasMenu.zip also contain executables for the required platform. Please remember to use "binary" mode when transferring these files between systems. Check that the file size is the same before and after transfer.
Any comments, suggestions or questions about the package may be directed to the author at "rasmol@ggr.co.uk".
Copyright (C) 1992 Norimasa Yamazaki
Permission to use, copy, and distribute this software and its documentation for any purpose without fee is hereby granted under the restriction of ORTEP-II, provided that the above copyright notice and this permission notice appear
in supporting documentation.
This software is provided "as is" without express or implied warranty.
Adapted to Macintosh by
Norimasa Yamazaki
University of Electro-Communications
Department of Physics and Chemistry
1-5-1 Choufugaoka
Choufu-shi
Tokyo 182
JAPAN
e-mail: yam@crystal.pc.uec.ac.jp
Original ORTEP-II was developed by
Johnson, C. K.
Report ORNL-5138
Oak Ridge National Laboratory
Oak Ridge, Tennessee, USA
This ORTEP runs on Macintosh series, which is equipped with 68020(30) CPU, FPU, a printer of 300 dpi resolution and System Software 6.07 or later.
This is a Macintosh hypercard stack explaining world map projections used by the USGS.
UnitCell is a program which runs on Macintosh computers and (in a more rudimentary fashion) under Windows. It refines cell parameters from powder diffraction data. Unlike most existing cell refinement programs it does not require initial estimates for cell constants; it uses a non-linear least squares method, which allows the refinement to be carried out on the actual observed data (e.g. two- theta in the case of angle-dispersive monochromatic diffraction, energy in the case of energy-dispersive diffra ction). Furthermore, the program incorporates regression diagnostics, particularly deletion diagnostics, to aid in the detection of outliers and influential data which could be deleterious to the regressed results. These diagnostic tools are particularly valuable in assessing the sensitivity of the calculated results to the observations of individual Bragg peaks.
The method and implementation are described in the following paper:
T J B Holland and S A T Redfern (1997) "Unit cell refinement from powder diffraction data: the use of regression diagnostics". Mineralogical Magazine 61: 65-77.
If you have trouble downloading from the above link, try http://www.ccp14.ac.uk/ccp/web-mirrors/crush/astaff/holland/UnitCell.html
Amph-base, a Macintosh hypercard stack based on emp-amph, is a database of amphibole compositions from Deer, Howie and Zussman, An Introduction to Rock Forming Minerals (1st ed.)
Hyperform is an interactive Macintosh program written in hyperscript which permits the input and calculation of a mineral formula from wet chemical and electron microprobe analysis. It also includes autosaving of data, search a nd sort routines, etc. The calculated formula can be exported to word processing, spreadsheet programs, or graphing programs.
Interactive, 3D Molecular Modeling Curriculum Development Program, featuring a Video Animation Generation Program, and a Molecular Image Database.
Molecular Ventures, Inc.
MacMolecule and PCMolecule create 3D-images of molecules for use in teaching molecular structure to students of biology, chemistry, and allied fields.
LatticeMaker can be used with Ball & Stick, Chem-3D and MacMolecule to help in the production of images of large bulk structures or super-structures of crystal lattices.
EQS4WIN Chemical equilibrium solver
Download from http://www.mathtrek.com/
EQS4WIN Chemical equilibrium solver
Download from http://www.mathtrek.com/
Gresens is a Macintosh program to calculate and plot mass balance changes, usually during alteration of rocks.
This program is by:
and was published in Computers and Geosciences. v. 19. (9). p. 1229-1238. 1993.
CET89 for the Mac
Many chemists and chemical engineers are familiar with the NASA chemical equilibrium code by Gordon and McBride. Dating from the early 1970's, this FORTRAN program remains a popular tool for solving complex chemical equilibrium problems. A Macintosh vers
ion of this program, called CET89 for the Macintosh, is now available. CET89 for the Macintosh is based on the FORTRAN source code (available from the University of Georgia), by B.J. McBride. Details of the hardware requirements, and some of the features
of CET89 for the Macintosh, are listed below. If you would like a free copy of CET89 for the Macintosh, version 1.2.1, please contact:
Alan S. Feitelberg
***Please provide your US mail address. CET89 is distributed ONLY on disk via
the US Mail.***
Feel free to distribute this message to anyone who might be interested in receiving a copy of CET89 for the Macintosh. Although CET89 for the Macintosh is distributed without charge, it is not public domain software, and remains copyright 1994 General El
ectric Company.
HARDWARE REQUIREMENTS
The URL is: http://www.geol.uni-erlangen.de/macsoftware/seditools/
Send me an e-mail if you observe any bugs or if you want to suggest improvements or additional tools.
Rainer Petschick
Seismic Duck is an entertaining but educational title for PowerPC Macs that educates you on how seismic waves are used to find oil underground. The easier levels are basic enough for elementary school children, while the upper levels are challenging enough for even professionals familiar with geophysics. The object is to help the duck find oil before going broke.
SOLVCALC. Save in a new folder that you create. Upon running sv2.exe it will automatically create a variety of files. Two are of interest. one is the Solvcalc.exe which is the program you want, the other is solvcalc.htm which you should open first and gives you instructions. This should be referenced to:
Wen, S.and Nekvasil, H. (1994) SOLVCALC: An interactive graphics program package for calculating the ternary feldspar solvus and for two-feldspar geothermometry. Computers & Geosciences 20, No. 6, 1025-1040.
Professor Hanna Nekvasil
Roger Nielsen's phase equilibria programs for modeling magmatic differentiation are described in Geochimica Cosmochimica Acta and in Reviews of Mineralogy, vol. 24.
The fortran source codes, and PC-executables are available in uuencoded format; a fortran compiler should allow you to run these programs on the platform of your choice.
On your browser, the files may be unformatted (lacking line breaks). To view the files as formatted documents, use the "view sources" feature on your browser, or download the files and look at them in a text editor using a monospaced font.
To decode the uuencoded binaries, you will need a uudecoder program, unless your web browser has one built in.
BLF.DAT
PETRO.CALC.PLOT is a package of macros that run in Microsoft
Excel 3.0 and 4.0 for Macintosh and PC computers. The macros have also been
written to run in Microsoft Excel 3.0 and 4.0 for Windows . (only the Mac versions are uploaded on this site right now; contact Gary Sidder if you need them). PETRO.CALC.PLOT
minimizes repetition and time required to recalculate and plot whole-rock
oxide data for petrologic analysis. Macros provided in PETRO.CALC.PLOT
normalize w hole-rock oxide data to 100 percent, calculate the cation
percentages and molecular proportions used for normative mineral
calculations, compute the apices for common ternary diagrams, determine
sums and ratios of specific elements of petrologic interest, and plot 33
X-Y graphs and five ternary diagrams. PETRO.CALC.PLOT may also be used to
create other diagrams as desired by the user.
Potdevin Jean-Luc
Universite des Sciences et Technologies de Lille
UFR des Sciences de la Terre
Laboratoire de Sedimentologie et Geodynamique
59655 Villeneuve d'Ascq Cedex
Tel: 20 43 47 54
Fax: 20 43 49 10
Email: Jean-Luc.Potdevin@univ-lille1.fr
GE Corporate R & D
Bldg. K-1, Room ES 122
1 River Road
Schenectady, NY 12301
Phone: 518 387-5737
FAX: 518 387-7258
Internet E-mail: feitelberg@crd.ge.com
FEATURES OF CET89 FOR THE MACINTOSH
Alan S. Feitelberg
GE Corporate R & D
Bldg. K-1, Room ES 122
Schenectady, NY 12301
feitelberg@crd.ge.com
A collection of free small applications to convert or calculate some things as used in sedimentology
SediTools are in Beta stage (0.9b1). Some new features and functions may be added in next versions.
e-mail: Petschick@em.uni-frankfurt.de
Seismic Duck 1.4 (PPC)
SOLVCALC
Department of Geosciences
State University of New York
Stony Brook, NY 11794-2100
U.S.A.
email: hnekvasil@notes.cc.sunysb.edu
Roger Nielsen's magmatic differentiation programs BLF and MIXNFRAC
Here's information on running the programs: Readme - BLF and Mixnfrac
Below are links to the files.
BLF.FOR
BLFEXE.uue
MIXNFRAC.DAT
MIXPLOT.uue
MIXNFRAC.FOR
mixnfracexe.uue
NEWDS3.DAT
RANDOM.DAT
MIXNFRAC.OUT
petro-calc-plot
Petro.Calc.Plot
Gary B. Sidder
U.S. Geological Survey
Denver Federal Center
Box 25046, MS-905
Denver, CO 80225-0046
303-236-5607/FAX 303-236-5603
gbsidder@greenwood.cr.usgs.gov
B. Saini-Eidukat
updated April 23, 1999