GEM-Selektor: Documentation

To start working with GEM-Selektor and perform exciting geochemical calculations, you'll need to familiarize yourself with the graphical user interface. Frequent tasks include:

1. Creating a Modeling Project:

   • Open GEM-Selektor and click on "New Project" in the Modeling Projects window.
   • Name your project and select the appropriate thermodynamic database.
   • Choose your system components, relevant elements, to automatically include relevant phases in your project.

2. Performing Process Calculations:

   • Use the built-in tools to simulate various geochemical processes, such as dissolution, precipitation, sorption, fluid-rock interactions, cooling, fluid mixing, and leaching.
   • You can model reaction paths, titrations, and other mass-transfer processes by setting up the system's bulk composition and constraints.

3. Making Changes to Thermodynamic Data:

   • Modify the thermodynamic database by adding or removing species and phases relevant to your specific project.
   • Ensure that the changes are reflected in your project's calculations by updating the database files in the appropriate folder.

Important folders

When working with GEM-Selektor two folder locations are important:

(1) GEMS Program folder containing the executable code, the default database files, and resources. Here you find the DB.default folder where you need to copy any third-party databases you plan to use to create new modeling projects.

(2) GEMS Projects folder containing test projects that come with the installation and all user projects. You can exchange projects with others by sending or receiving projects folders.

WindowsMac OS XLinux

Folder Path	Description
C:\'your_user'\ GEMS3.9.x\Gems3-app\	Program folder
C:\'your user'\ GEMS3.9.x\Gems3-app\Resources\	Resources folder, here you also have the doc folder with documentation help files \doc\html\
C:\'your user'\ GEMS3.9.x\Gems3-app\Resources\DB.default\	default databases, these are available when creating a new project. Copy here any third-party database (e.g., cemdata) and you will be able to use it for creating a new project
C:\'your user'\ Library\Gems3\Projects\	Projects Folder: This is where the test and user projects are stored. To add a shared project, simply copy the project folder here, and it will appear in the Open/New projects list when you open GEM-Selektor. To share your project, zip the folder and send it to someone else. They will need to unzip and copy the project folder into their GEMS projects folder.

Folder Path	Description
/Applications/ Gems3.app/Contents/	Program folder
/Applications/ Gems3.app/Contents/Resources/	Resources folder, here you also have the doc folder with documentation help files /doc/html/
/Applications/ Gems3.app/Contents/Resources/DB.default/	default databases, these are available when creating a new project. Copy here any third-party database (e.g., cemdata) and you will be able to use it for creating a new project
/Library/ gems3/projects/	Projects Folder: This is where the test and user projects are stored. To add a shared project, simply copy the project folder here, and it will appear in the Open/New projects list when you open GEM-Selektor. To share your project, zip the folder and send it to someone else. They will need to unzip and copy the project folder into their GEMS projects folder.

Folder Path	Description
~/'your_user'/ GEMS3.9.x/Gems3-app/	Program folder
~/'your user'/ GEMS3.9.x/Gems3-app/Resources/	Resources folder, here you also have the doc folder with documentation help files /doc/html/
~/'your user'/ GEMS3.9.x/Gems3-app/Resources/DB.default/	default databases, these are available when creating a new project. Copy here any third-party database (e.g., cemdata) and you will be able to use it for creating a new project
~/'your user'/ Library/Gems3/Projects/	Projects Folder: This is where the test and user projects are stored. To add a shared project, simply copy the project folder here, and it will appear in the Open/New projects list when you open GEM-Selektor. To share your project, zip the folder and send it to someone else. They will need to unzip and copy the project folder into their GEMS projects folder.

Help contents

The most direct way to get information about anything in GEMS is to use its content-aware help interface. This can be accessed from anywhere in the code by pressing F1 (on Mac using the keyboard shortcut Command (⌘) + Shift + ?) or the "Help" button . This will open the help window with context-specific information about the current window.

Test projects

The GEM-Selektor comes with a suite of test modeling projects. These are included in the GEMS3 installer (see Gems3-app/Resources/projects/) and will be automatically copied to the user projects directory (e.g., /Library/Gems3/projects/) upon the first installation. The test projects address specific problems and can help you learn how they were defined, serving as a starting point for your own modeling applications. Plan to model something similar, you can clone the project, re-name it, and adapt it to your specific system. Before diving too deep into these projects it is expected that you gained some basic knowledge on using GEMS.

Description of Models

The thermodynamic methods formulations that are available GEMS are described bellow and in files found in the Gems3-app\Resources\doc\pdf subfolder of your installed GEM-Selektor folder.

File	Description
Temperature Corrections Pressure Corrections	Built-in models for temperature and pressure corrections for thermodynamic properties calculated in the GEM-Selektor code from data in DComp records
Temperature Corrections Reactions	Methods for temperature corrections for thermodynamic properties calculated in the GEM-Selektor code from data in ReacDC records
Activity models	Models for calculation of activity coefficients for aqueous species and solid-solution end-members (with setup codes in Phase records)
Multisite Mixing models	Models for calculation of activity coefficients and configurational terms for multi-site (sublattice) solid solution models.
Surface complexation models	Description of setups and built-in calculations related to GEM SCMs (surface complexation models) Will be updated soon with ClaySor model for sorption of cations on clay minerals and clay rocks.
Non-electrolyte fluids	Contribution by S.V.Churakov: Description of built-in temperature, pressure and composition corrections of molar thermodynamic properties of non-electrolyte fluids and their mixtures.
Kinetics	A progress report describing how mineral-water reaction kinetics (with trace element uptake kinetics) can be modelled with GEM-Selektor code.
Chemical equilibrium	A short article describing how the chemical equilibrium partitioning can be efficiently modelled with GEM-Selektor code, with special reference to two solid-solution aqueous solution systems relevant to nuclear waste disposal, as well as the status and the perspectives of development of the GEMS.

Workshops and tutorials

Have a look at the schedule for future workshops or the available online recordings. There are several materials and tutorials available on how to use GEM-Selektor to model cementitious systems and fluid rock interaction at hydrothermal conditions.

Discussion

If you have an idea, an example to share participate in the discussion.