module 1: creating your first project in gems and ... · fig. 1: the mines thermodynamic database...

GEMS Tutorial, A. Gysi, D. Kulik and D. Miron August 2018

MODULE 1: CREATING YOUR FIRST PROJECT IN GEMSAND INSTALLING THE MINES DATABASE

GEM-Selektor (GEMS), is a numerical modeling program with a graphical userinterface based on Gibbs energy minimization and permitting to calculate and solvefluid-rock interaction problems of interest in geochemistry. Installation instructions forGEMS can be found at http://gems.web.psi.ch/GEMS3/techinfo.html.

Here we will learn to create a new Project, the selection of thermodynamic databases,components and equations of state for your modeling project. We will also explain theproject folder structure and how to install the MINES thermodynamic database formodeling hydrothermal fluid-rock interaction and ore-forming processes http://tdb.

mines.edu. You will also learn how to interact basalt with water in your first equilib-rium calculations.

Installing the MINES17 thermodynamic database

The MINES17 database can be downloaded at http://tdb.mines.edu, (Figure 1) orfound on your memory sticks under MINES-TDB.

1. Download and unzip the DB17.default archive.

2. Merge the database files with the Resources/DB.default folder (Figure 2). To doso, copy the 12 files within the folder to the DB.default folder of your gems3.appinstalled subfolder by copying-pasting the 12 files with .pdb and .ndx extensions.

In Linux this folder is in /Gems3-app/Resources/DB.default; In Mac OSX thisfolder is in /Applications/gems3 then right-click show package content and go toContents/Resources/DB.default; In Windows this folder should be in /Gems3-app/Resources/DB.default.

The folder structure of the GEMS program, independent of the operating systemused, consists of two main folders:

• Gems3-app

– The GEMS3-app folder contains the program resources and also a sub-folder Resources/DB.default, which will be used to copy the MINESthermodynamic database files into it.

• Library/Gems3/projects

– The projects folder will contain all the projects you create and work on,and will also be the folder in which you can copy the tutorial folders.

1

http://gems.web.psi.ch/GEMS3/techinfo.html

http://tdb.mines.edu




Download the DB17.default archive file

Fig. 1: The MINES thermodynamic database webpage and files to download.

Creating a new project from scratch

1. Open GEMS and click New Project in the Modeling Projects window. Give aname to your project (no spaces). The user interface is shown in Figure 3.

2. In the next window, you can choose the thermodynamic database for your projectFigure 4. Select the database files 3rdparty/MINES and the support file anddeselect other databases. Click next.

Do not forget, you have an extensive list of minerals included in this database.Once you have gone through the tutorials and are familiar with GEMS, I suggestthat in thermodynamic database mode you switch to the ”Phase” module (Fig-ure 7), and delete minerals that are not relevant for your own specific project.Also, for less advanced users, I suggest not using the feldspar solid solution model(ss) but only their end members (i.e., anorthite, albite and microcline).

3. In the next window choose your system components, i.e. H-O-C-Cl-Na-K-Ca-Mg-Al-Fe-Si-Ti (Figure 4). By doing so, GEMS will automatically look up allphases with these components in the MINES17 database and copy them intoyour modeling project! Remember? all your modeling projects you are workingon are located under Library/Gems3/projects...

2


Choosing an activity model for aqueous species and EOS for gases

In the next window, you will be able to choose the activity model for your aqueousspeciation calculations (e.g. Debye-Hueckel, Davies equation, ...), and the EOS for thegases.

1. For now, follow Figure 5 using the extended Debye-Hueckel equation (Helgeson),check the parameters and click Check for the aqueous speciation model. Thismodel is ideal for modeling H2O-NaCl aqueous solutions (an other backgroundelectrolyte) at hydrothermal conditions at relatively moderate salinities observedin many ore deposits.

2. Then you can switch to the gas EOS model tab and choose the Peng-Robinson-Stryjek-Vera (PRSV) model and click Check (Figure 5). That’s it! Now you areready to model your first equilibrium model!

Note: this model is for non-ideal gases, and for this purpose a new phase with theacronym (f) was added to the MINES database with all the relevant parametersusing the PRSV EOS. Else the choice would be the ideal gas law with a phaseusing the acronym (g).

Your first fluid-rock equilibrium model

In the next window, you will be able to define the name of your first fluid-rock equi-librium (SysEq) calculations and set the pressure and temperature of your system(Figure 6).

1. Add a name without spaces and P-T conditions, i.e. we choose basalt-fluid, 350◦C for T and 1 kbar for P.

2. Next window we select our ingredients and add 1000 g of H2O (Aqua), 10 g ofNaCl, 5 g Gas CO2 and 200 g of basalt (Figure 6). Click Ok.

3. Finally, you can click on Calculate BCC followed by Calculate equilibrium

with GEM as shown in Figure 7.

3


a) Copy 12 files from the DB17v.1.default folder

b) Paste 12 files into GEMS3-app/Resources/DB.default

Fig. 2: User interface showing the files of the unzipped DB17v.1.default folder. Note the MINESdatabase will only appear under 3rd party once it has been added to your Resources/DB.defaultfolder.

4


Fig. 3: User interface showing the Modeling Projects window where you can a) create a new projectby clicking on New Project, or b) open and existing project in the list. If you cannot see this windowbecause GEMS is open, toggle between System Equilibria and Thermodynamic database modes(Figure 7).

5


Select thermo database

Select your system composition

Fig. 4: User interface showing the windows to select the thermodynamic database, and the compo-sition of the system to be modeled. Note the MINES database will only appear under 3rd party onceit has been added to your Resources/DB.default folder.

6


a) select PRSV

b) click to apply

a) Select an activity model for aqueous speciation

c) click to apply

b) Select the right parameters

d) EOS model for gases

Fig. 5: User interface showing the windows to select the activity model for the aqueous speciationand the EOS for gases.

7


a) Select a name

b) P-T conditions

a) Select rock, fluid

b) Select quantity, units

Fig. 6: User interface showing the windows to create a new equilibrium system and define P-Tconditions of our first calculation.

8


a) Calculate BCC b) Calculate equilibrium

with GEMEquilibrium calc mode

Thermo dtb mode

Add/remove phase

Thermo data MINES17

Fig. 7: User interface showing how to Calculate BCC followed by Calculate equilibrium with

GEM. Also shown the Equilibrium Calculation Mode and the Thermodynamic database mode, whereyou can inspect the MINES17 database.

9

module 1: creating your first project in gems and ... · fig. 1: the mines thermodynamic database...

Documents