GEM-Selektor is a Gibbs Energy
program package for interactive thermodynamic modeling of
heterogeneous aquatic (geo)chemical systems, especially those involving
metastability and dispersity of mineral phases, solid solution -
aqueous solution equilbria, and adsorption/ion exchange.
Includes a built-in (default) thermodynamic database in both
thermochemical and reaction formats, and an advanced multi-document
graphical user interface with a context-sensitive help system.
What is GEM-Selektor?
GEM-Selektor v.3 (GEMS3)
is a geochemical modelling code. It uses
an advanced convex programming method of Gibbs energy minimization
implemented as an efficient Interior Points Method (IPM) in the GEMS3K kernel
Using GEMS3, you can
compute an equilibrium phase assemblage and speciation
in a complex chemical system with many phases-solutions from its total
composition at given temperature and pressure (optionally,
subject to additional kinetic metastability constraints).
- TSolMod The code includes a TSolMod library of built-in phase
of non-ideal mixing, relevant to a wide range of applications in
involving solids, solid solutions, metls, gas/fluid mixture, aqueous
electrolyte, (non-)electrostatic surface complexation, and ion
exchange can be considered simultaneously in the chemical
elemental stoichiometry (+ electrical charge) of the system, i.e.
any mass balance constraints for ligands or
GEMS3 package includes
a built-in write-protected default chemical
thermodynamic data base, selected
parts of which are
automatically copied into your modelling project
base upon creation of the modeling project, where the thermodynamic and
compositional input data are
immediately available for calculation of equilibrium states. This data
base can be extended or corrected at any time, and
changes will have no effect on the default database supplied with the
Within a modeling project, all you have to do
is, in principle, to provide a recipe, i.e. the bulk composition of
your system and, possibly,
exclude some irrelevant species and phases and set mestability
constraints, then start GEM calculation of equilibrium state.
If necessary, the
standard-state thermodynamic data will be automatically converted
to temperature/ pressure of interest before computing
the equilibrium state using several techniques as appropriate for
soilds, gases, aqueous and surface species.
Using GEMS3, you can
simulate various mass-transfer processes and reaction paths,
such as titrations, mixing, weathering, or sequential reactors,
by a "process extent" master variable(s) used in the process
simulator scripts. Results of such "process simulations"
can easily be tabulated, plotted (also at run time), copy-pasted to
other programs, or
printed into text files.
In addition to the
common "primal solution", i.e. equilibrium chemical speciation, the GEM
IPM algorithm always
calculates a "dual solution", i.e. chemical
potentials of stoichiometry units (elements) in equilibrium state. By
comparing primal and dual solutions, it becomes easy to
retrieve pe (Eh), pH, fugacities of gases, very low activities or
concentrations of dissolved species, as well as to estimate unknown
properties of mixing or of end-members in a solid solution - aqueous
Overall, using the
code will bring you all the power of advanced chemical thermodynamic
modelling, leading to high efficiency in interpreting even complex
hydrothermal aquatic systems. Of course, some learning and exercise
will be needed. To make it easier, we strive to provide a help tutorial
and a set
of test projects .
What is GEM-Selektor not?
GEMS3 cannot replace your knowledge
possible to set up meaningful problems in geochemical
thermodynamic modelling and interprete results without a good
of aquatic chemistry and chemical thermodynamics, even though
the underlying concepts are very general and quite simple.
Taking a course in the above subjects and/or reading a few good
textbooks such as (Anderson, 2005; Nordstrom and
Muņos, 1994; Stumm and Morgan, 1996) would therefore be a
investment, helping you to maximize the usefulness of GEM modeling.
GEMS3 is not a substitute for
thermodynamic modelling (as almost any modelling) should be
regarded as nothing else than a tool helping
you in interpreting your geochemical data and in reaching a deeper
understanding of how the chemical system works. As with any
tool, using GEMS3 can be either creative or a waste of time.
GEMS3 cannot formulate chemical
problems and interpret results.
GEMS3 modeling runs yield rather unexpected results, urging a
re-consideration of some concepts or assumptions.. This is
normal; a few more modeling iterations will soon give you much more
confidence in your data and model predictions. It makes no
sense is to start modeling just having the raw data,
without a working hypothesis to be verified;
clearly, no interpretation of results is possible in this case.
GEMS3 is just a tool for checking
how realistic your ideas about the system are.
GEMS3 cannot simulate
processes in far-from-equilibrium systems.
biological or technical systems, especially at short time
scales, exist far from equilibrium or in a transient state. In such
cases, fundamental assumptions about local and partial
equilibria cannot be applied and, therefore, methods of
equilibrium chemical thermodynamic cannot be used. Before
doing any model
calculations with GEMS or another speciation code, first question to
ask is whether the concept
local/partial equilibrium is adequate for the system of interest.
GEMS3 is not a tool for
plotting phase diagrams.
diagrams is a popular exercise in chemical thermodynamics in
petrology or metallurgy, and in aquatic chemistry as well. This often
requires a very serious simplification of the chemical system (to make
observable in 2D or 3D coordinate space). A number of tools is
avaialble for this purpose (Perplex, Thermocalc, PHREEQPLOT etc.). GEMS3
modeling, however, is aimed at
quantifying the effects of equilibration at given (sequence of) T,P,
and bulk composition in full speciation complexity of the system,
perhaps under many additional kinetic, metastability
and/or dispersity constraints. GEMS3 batch calculations can be designed
in a way that
directly produces phase, activity, or reaction-path diagrams.
GEMS3 cannot create
thermodynamic data or assess their quality.
strong as it's weakest link. Likewise, any modeling
result is not better than the input compositional and thermodynamic
data. In the past 30 years, a considerable progress has
been made in compilation of internally consistent thermodynamic
data bases, including those supplied as the default
the GEMS3 code. However, no database covers everything relevant for all
possible applications. Therefore, it is usually
necessary to extend it with the standard-state data for some
missing species or minerals, or extend T,P correction range. Although
GEMS3 provides a number of tools for extension of the project
thermodynamic database, it cannot replace an expert in
critical compilation, matching and retrieval of thermodynamic data.
Some practical features
In most geochemical
modelling studies (except maybe simple test examples) the user will
to extend thermodynamic database with some new chemical
species and phases, or change some thermodynamic properties
of them in a consistent way. A modeling project concept
implemented in GEMS3 lets the user performing such modifications
and continue thermodynamic modeling straight away: already created
input chemical recipes and output equilibrium speciation will be
updated or extended automatically.
All input data and
of GEM calculations are automatically stored in the modeling
project data base files and nowhere else. The user can zip her
modelling project folder for back-up or to share it
with colleagues. Anyone who has (the same or newer) GEMS3 code installed
on her PC can
unpack that project and run it, as the user would continue running it
on her own desktop.
GEMS3 has a
structure of thermodynamic database. The standard molar data for
chemical species are kept either in thermochemical
equation-of-state) DComp format, or as reactions defining
standard molar properties
of a given species via that of the
reaction and of other species involved (ReacDC format). In both
formats, many data
consistency checks are performed. Data of both
formats, saved into database records, can be immediately used in GEM
calculations of chemical equilibria.
Unlike command-driven or batch-input-file geochemical codes
(e.g., PHREEQC, EQ3/6, GWB, ChemApp, Selektor-C, HCh), GEM-Selektor is
modular package in which computational modules share data
objects in memory, manipulated by the data base maintenance module.
GEMS3 is written in C/C++ and has a modern multi-document
mouse-menu-driven GUI (graphical user's interface) based on the Qt GUI Toolkit, which also
provides GEMS3 with
cross-platform portability: The source code of GEMS3 can be
compiled and executed on most Intel-based Linux/Unix, Windows, and Mac
OS X desktop platforms.
In GEM-Selektor, no
files with input data are necessary. The program operation is
fully interactive, controlled
by mouse clicking on toolbar icons or menu items, selecting record keys
from lists, or entering data directly into spreadsheet-like screen
forms. Your entered or calculated data is automatically stored
in the project data base, where it is kept accessible for
subsequent calculations or data sampling, plotting or exporting.
This interactive functionality makes the work flow of geochemical
modeling more efficient than ever before.
Almost all kinds of
accessible in GEM-Selektor windows using the data object labels can be
printed into ASCII text files using the simple print
A collection of template printing
scripts is provided for the user' convenience; all scripts can
easily be customized and saved into your project data base. The data in
module window pages can also be copy-pasted to/from most other
spreadsheet or text editing programs. Some results of computations can
also be exported into csv and VTK format files.
GEM-Selektor GUI provides the user with a context-sensitive
hypertext runtime help. In most cases, the tooltips (popping up upon
hovering the cursor over almost
every button or data field) are sufficient. Direct access to separate
HelpWindow with documentation is possible from
any dialog, screen form, and even a single data field cell on any
screen form. The HelpWindow has the industry-standard browsing and
kernel GEMS3K implements an
Interior Points Method (IPM) module for non-linear
minimization of total Gibbs energy of the heterogeneous multi-phase
chemical system (more...), with improved
accuracy, mass balance precision, convergence, speed, and extended
input data diagnostics
the needs of the reactive-transport modelling applications in
performance assessment of radioactive waste disposal, aquatic
chemistry, and hydrogeochemistry. The IPM module uses fast and
efficient linear algebra solvers from the JAMA C++ TNT package
standalone program implementing the enhanced GEM IPM algorithm is now
available open-source from this
web site under the LGPL v.3 license. GEMS3K has no GUI and can
read/write input/output data from/to text files, as well as exchange
the data in computer memory. It can also interpolate thermodynamic data
for chemical species for changing temperature and/or pressure. The
purpose of GEMS3K is to facilitate and promote development of coupled
codes for modelling reactive mass transport
using the "operator splitting" approach with GEM chemical equilibria
solver. GEMS3K C/C++ code is small, fast, and meets all requirements of
coupled codes including MPI parallelization and high-performance
computing for realistic 2D or 3D transport simulations.
- Kulik D.A., Wagner T., Dmytrieva S.V., Kosakowski G., Hingerl
F.F., Chudnenko K.V., Berner U. (2013): GEM-Selektor geochemical
modeling package: Numerical kernel GEMS3K for coupled simulation codes.
Computational Geosciences, 17(1), 1-24. doi.
- Karpov I.K., Chudnenko K.V., Kulik D.A., Avchenko O.V. and
Bychinski V.A. (2001). Minimization of Gibbs free energy in geochemical
systems by convex programming. Geochemistry International 39(11),
- Karpov I.K., Chudnenko K.V. and Kulik D.A. (1997): Modeling
chemical mass-transfer in geochemical processes: Thermodynamic
relations, conditions of equilibria and numerical algorithms. American
Journal of Science 297 (October), 767-806.
Last updated: 30.04.2013
(c) 2003-2013 GEMS Development Team.