This document is a brief guide to the installation and usage of OrganoBIoGeoTherm (or OBIGT) for Windows. OBIGT provides a graphical frontend to SUPCRT92, enabling the user to calculate as a function of temperature and pressure the standard molal thermodynamic properties of aqueous, solid, and gaseous species and reactions between them.

OBIGT-1.52.zip

(size: ~5.7 Mb, date: 1999/06/21) Download this file to your desktop, unzip by double-clicking on it, and proceed to run the "setup.exe" program in the newly formed directory. The program and datafiles should be automatically installed to your computer. There is no need to separately install SUPCRT92.

OBIGT was developed in 1996-1999 by John J. Donovan for Prediction Central. Note that updated datafiles can be imported to OrganoBIoGeoTherm's substance database; see Updating the Substance Database, below.

Quick Start

• Start the program, and you will see the OBIGT root window in the background and the Basic Calculations window in the foreground (screenshot). Here, you choose one of three default reaction configurations, or temperature-pressure grids. The two buttons at the bottom allow you to Create and Run a chemical reaction.
• Click the Create Reaction button to get to the Reaction Parameters window. Enter in the coefficients for a reaction of interest, say one representing the weathering of potassium feldspar: 2KAlSi3O8 + 2H+ + H2O = Al2Si2O5(OH)4 + 2K+ + 4SiO2 (screenshot). A few notes about this window:
  • After selecting a species from the field on the left side of the window, use the Add Reactants and Add Products buttons, and their Remove counterparts, to adjust the reaction coefficient of the selected species by +/- 1.
  • If you want to enter the reaction coefficient manually, be sure to click the OK button next to the entry field, as typing Enter does not register the updated value. Also note that the coefficient on liquid H2O (water) is controlled by the forms at the bottom of the window.
  • It is possible to enter a reaction that is not balanced with respect to mass or charge. Although it may be possible for OBIGT to use the chemical formulas provided in the SUPCRT data file to check the reaction balance, in practice it is convenient to be able to specify a "reaction" with only a single species as product, in order to calculate that species' properties.
  • Clicking OK will take you to a prompt to save the reaction settings to a file (call it trash.rxn for this example). If it is successfully saved, the contents of the file will be echoed to the OBIGT root window and the Reaction Parameters window will close.
• Back at the Basic Calculations window, click Run Reaction. The results of the SUPCRT run will be sent to the output window. This text can be pasted into spreadsheets or other documents.
• Access the other OBIGT windows, including Substance Database and Advanced Calculations, using the Window menu of the root window.

Updating the Substance Database

• Before making any changes to the database, make a backup copy of the file C:\Program Files\OrganoBioGeoTherm\ORGANOBIOGEOTHERM.mdb in case you want to recover the default OBIGT database.
• The Substance Database window provides an interface to manage a Microsoft database (*.mdb) containing thermodynamic data. It is accessed from the Window menu of the OBIGT root window (screenshot). When it first opens, you are prompted to "Open Old Substance Database"; at this point, select the file ORGANOBIOGEOTHERM.mdb.
• As you change substance data, the database is automatically updated, so before closing the Substance Database window, nothing is required to save your changes to the *.mdb file (i.e., there is no "Save" button).
• However, after any updates to the *.mdb file, you must perform TWO exports for the updates to be seen by OBIGT and the SUPCRT program that calculates the reaction properties.
  • Click File > Export, and save to file DPRONS92.dat. Click Yes when asked if you want to replace the existing file.
  • Click File > Export, and save to file ORGANOBIOGEOTHERM.dat. Click Yes when asked if you want to replace the existing file.
• The database that comes with this version of OBIGT contains 179 minerals, 16 gases, and 294 aqueous species. It thus appears to be equivalent to the sprons92.dat datafile that appeared in SUPCRT92. To use another datafile, (an updated one is here), take these steps.
  • Close the current database by clicking File > Close in the Substance Database window.
  • Click File > New, and create a new database named something like slop98.mdb. Click OK for the message about "standard database updated for new tables and fields" and on the file information window.
  • Click File > Import, and select the path to slop98.dat.
  • A popup window asks you for the number of comment lines to skip in the import file. Provide the appropriate number (the number should be given in the last line of the SUPCRT file you are importing).
  • After successful completion of the import, export the *.mdb database to DPRONS92.dat and ORGANOBIOGEOTHERM.dat as described above. On your next visit to the Reaction Parameters window, you should find all the new species.
• To recover the original OBIGT database, first click on File > Close, then File > Open, and browse to the ORGANOBIOGEOTHERM.mdb file you backed up. Then, export this to DPRONS92.dat and ORGANOBIOGEOTHERM.dat as described above.

Bugs

• If you use the second configuration option of Basic Calculations ("Use 0 to 1000 C at 100 C increments and from 500 to 5000 bar at 500 bar increments across the single-phase regions of water (GRID.CFG)."), the reaction properties as a function of temperature and pressure do not appear in the output file. (The headers, including reaction and species information and the reaction properties at 25 C and 1 bar are present.) (reported by T. Wagner, 2006)

This appears to be a complication of the option to generate plot files in SUPCRT. A workaround is to first set up and run the calculation using OBIGT (even though the calculation does not finish, this action prepares the input files for SUCPRT). Then, edit the SUPCRT.INP file in the OBIGT directory (C:\Program Files\OrganoBioGeoTherm\) as follows: change the "3" to "1" in the second to last line, and delete the last line. The file should now look like:

  n
  supcrt.dat
  2
  supcrt.cfg
  1
  supcrt.rxn
  supcrt.out
  1

The effect of this is to say "no" to plot file generation during the scripted session with SUPCRT. Save this file. Then, using Windows explorer or a command prompt, execute RUN.BAT in the OBIGT directory. The full results should be written to supcrt.out (note that the results will not be shown on the OBIGT main window).

• Database operations fail if the operating system language is not English (reported 6/2007).

Substance records in SUPCRT datafiles contains a datecode (e.g. 14.Jul.07) indicating when the record was updated. Because of language-specific representations of dates, the import of SUPCRT-format datafiles into OBIGT may not work if Windows is configured with a language other than English. A workaround is to temporarily set the language of the operating system to English while importing or exporting OBIGT database files.

• There may be others ...