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GWB Reaction Modeling Guide The Geochemist’s Workbench® Release 11 GWB Reaction Modeling Guide The Geochemist’s Workbench® Release 11 GWB Reaction Modeling Guide Craig M. Bethke Sharon Yeakel Aqueous Solutions, LLC Champaign, Illinois This document © Copyright 2016 by Aqueous Solutions LLC. All rights reserved. Earlier editions copyright 2000–2015. This document may be reproduced freely to support any licensed use of the GWB software package. Software copyright notice: Programs GSS, Rxn, Act2, Tact, SpecE8, Gtplot, TEdit, React, X1t, X2t, Xtplot, and ChemPlugin © Copyright 1983–2016 by Aqueous Solutions LLC. An unpublished work distributed via trade secrecy license. All rights reserved under the copyright laws. The Geochemist’s Workbench®, ChemPlugin™, We put bugs in our software™, and The Geochemist’s Spreadsheet™ are a registered trademark and trademarks of Aqueous Solutions LLC; Microsoft®, MS®, Windows XP®, Windows Vista®, Windows 7®, Windows 8®, and Windows 10® are registered trademarks of Microsoft Corporation; PostScript® is a registered trademark of Adobe Systems, Inc. Other products mentioned in this document are identified by the trademarks of their respective companies; the authors disclaim responsibility for specifying which marks are owned by which companies. The software uses zlib © 1995–2005 Jean-Loup Gailly and Mark Adler, and Expat © 1998–2006 Thai Open Source Center Ltd. and Clark Cooper. The GWB software was originally developed by the students, staff, and faculty of the Hydrogeology Program in the Department of Geology at the University of Illinois Urbana– Champaign. The package is currently developed and maintained by Aqueous Solutions LLC. Address inquiries to: Aqueous Solutions LLC 301 North Neil Street, Suite 400 Champaign, IL 61820 USA Warranty: The Aqueous Solutions LLC warrants only that it has the right to convey license to the GWB software. Aqueous Solutions makes no other warranties, express or implied, with respect to the licensed software and/or associated written documentation. Aqueous Solutions disclaims any express or implied warranties of merchantability, fitness for a particular purpose, and non- infringement. Aqueous Solutions does not warrant, guarantee, or make any representations regarding the use, or the results of the use, of the Licensed Software or documentation in terms of correctness, accuracy, reliability, currentness, or otherwise. Aqueous Solutions shall not be liable for any direct, indirect, consequential, or incidental damages (including damages for loss of profits, business interruption, loss of business information, and the like) arising out of any claim by Licensee or a third party regarding the use of or inability to use Licensed Software. The entire risk as to the results and performance of Licensed Software is assumed by the Licensee. See License Agreement for complete details. License Agreement: Use of the GWB is subject to the terms of the accompanying License Agreement. Please refer to that Agreement for details. Cover photo: Salinas de Janubio by Jorg Hackemann Contents Chapter List Introduction ........................................................................................... 1 Getting Started with React ..................................................................... 3 Tracing Reaction Paths ......................................................................... 17 Kinetic Reaction Paths ......................................................................... 57 Custom Rate Laws .............................................................................. 113 Using Gtplot ....................................................................................... 131 Appendix: Further Reading ................................................................. 141 v Detailed Contents Introduction ........................................................................................... 1 1.1 React program ......................................................................................................... 1 1.2 Gtplot program ........................................................................................................ 1 Getting Started with React ..................................................................... 3 2.1 Conceptual model ................................................................................................... 3 2.2 Example calculation ................................................................................................ 4 2.3 Initial system ........................................................................................................... 7 2.4 Redox disequilibrium ............................................................................................ 10 2.5 Activity coefficients ............................................................................................... 10 2.6 Sorption onto mineral surfaces ............................................................................ 10 2.7 Settable variables.................................................................................................. 11 2.8 Controlling the printout ........................................................................................ 14 2.9 React command line ............................................................................................. 15 Tracing Reaction Paths ......................................................................... 17 3.1 Titration paths ....................................................................................................... 17 3.2 Flow-through model ............................................................................................. 24 3.3 Flush model ........................................................................................................... 28 3.4 Polythermal reaction paths .................................................................................. 30 3.5 Buffered paths ....................................................................................................... 33 3.6 Sliding activity and fugacity .................................................................................. 36 3.7 “Flash diagrams” ................................................................................................... 43 3.8 Fractionation of stable isotopes ........................................................................... 47 3.9 Picking up the results of a run .............................................................................. 53 Kinetic Reaction Paths ......................................................................... 57 4.1 Setting kinetic reactions ....................................................................................... 57 4.2 Kinetics of precipitation and dissolution ............................................................. 61 4.2.1 Promoting and inhibiting species ............................................................................... 65 4.2.2 Nonlinear rate laws ...................................................................................................... 67 vii 4.2.3 Cross-affinity rate laws ............................................................................................... 69 4.2.4 Nucleation ................................................................................................................... 70 4.3 Forward and reverse reactions ............................................................................. 71 4.4 Kinetics of complexation and sorption ................................................................. 73 4.5 Gas transfer kinetics .............................................................................................. 80 4.6 Kinetics of redox reactions .................................................................................... 83 4.6.1 Catalysis on mineral surfaces ..................................................................................... 89 4.6.2 Enzymes and biotransformations .............................................................................. 93 4.7 Microbial metabolism and growth ........................................................................ 99 4.7.1 Metabolic rate ........................................................................................................... 100 4.7.2 Relationship to other rate laws ................................................................................ 103 4.7.3 Example calculation ................................................................................................. 104 4.8 Chaining together kinetic paths .......................................................................... 109 Custom Rate Laws .............................................................................. 113 5.1 Setting the rate law form directly ....................................................................... 113 5.2 Rate law scripts .................................................................................................... 114 5.3 Compiled rate laws .............................................................................................. 118 Using Gtplot ........................................................................................ 131 6.1 Initial plot ............................................................................................................. 131 6.2 XY Plot configuration ........................................................................................... 132 6.3 Plot types ............................................................................................................
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