Usage

In order to generate pseudosection (including isochemical phase diagrams) we provide a in-house GUI developped using MATLAB 2020b and tested on MATLAB 2019b.

Specifications

The GUI sends a list of pressure-temperature points to MAGEMin for a specified bulk-rock composition and receives back the stable phase mineral assemblage.
The GUI uses adaptive mesh refinement to refine the reactions lines.
Possibility to save and load pseudosection
Various display options including, stable phases, Gibbs energy, phase fractions, phase compositions (isopleth), densities etc…

KLB-1 Pseudosection tutorial

As a simple tutorial we present the necessary steps needed to produce a pseudosection for KLB-1 peridotite in the KNCFMASTOCr chemical system and from 0.0 to 50 kbar and 800 to 2000°C.

Sarting GUI

Using MATLAB (2019+) launch the GUI within MAGEMin working directory

cd /your_path_to_MAGEMin/MAGEMin_1.x/
run PlotPseudosection.mlapp

This opens the following window:

On the displayed window (simulation) you can choose and modifiy several parameters/options. First, you can change the name of the simulation (or save/load a pre-existing simulation)

Change the filename from “test” to “KLB-1_pseudosection”

Set P-T conditions

Below you can accept or modify the suggested pressure and temperature range. The step parameter defines the number of points along the pressure and temperature axes.

Use the default pressure and temperature range and change the pressure step to 4 kbar and the temperature to 100 °C

Choose bulk-rock composition

In the middle “Composition” panel you can either specify your own bulk-rock composition or access the in-built list of bulk-rock compositions

To load a custom bulk-rock composition you first need to create a file your_bulk.dat. The name of the file your_bulk will be used for the name of the pseudosection. The file has to be structured as follow:

your_bulk.dat:

SiO2	Al2O3	CaO	MgO	FeO	Fe2O3	K2O	Na2O	TiO2	Cr2O3	H2O
48.43	15.19	11.57	10.13	6.65	1.64	0.59	1.87	0.68	0.1	3.0

An example of custom bulk-rock composition is provided in /examples/bulk1.dat.
Note that instead of Fe2O3, you can directly provide O. If you provide Fe2O3 the GUI will internally convert it to FeOt and O.

Once the file is created you can load it using the button Load from file. Note that before loading your bulk-rock composition you first need to select the right system unit [mol or wt]. If the bulk-rock composition you provided is in [wt] it will be automatically converted to [mol], the system unit used in MAGEMin.

For for this tutorial, we will the use default option “pre-defined test 0” (KLB-1 peridotite)

Compute pseudosection

The set of parameters should look like this.

Click on “Start new computation” at the bottom of the “Thermodynamics” panel to launch the computation. If everything is correctly setup it should opens the folloying window

At the end of each refinement step, a set of 3 figures are displayed and updated. They show the “melt fraction”, the “adaptive mesh refinement” and “the number of stable phases”

Once the computation is over, the GUI displays the pseudosection. The number of minimization points is shown at the bottom right, for this example “3493 points”. Note that by default the number of stable phases is displayed together wit the mesh refinement grid. Note that, you are in the “Pseudosection” window.

Refine pseudosection

From there you can decide to refine the pseudosection as the resolution is rather low.

click on “Refine all phase boundaries” in the bottom right corner, and then “Start computation”

Change displayed field

Upon refinement you can choose to change the field that is displayed

To display the variance click on the “Plot color” menu and select “Variance”

To hide the mesh refinement grid click, set “Show edges” to “Off”, which gives

Display stable phases labels

In the bottom right menu, you can now access the plotting options

Tick “Add phase labels” and then click on the different fields to display the stable mineral assemblage directly on the grid such as

Note that the label box position, with respect to the field you click on, remains the same e.g. in a top-right position. If you miss-clicked and two boxes overlap, don’t panick, you can always click on “remove last label”, or even “remove all labels” and redo the process

Save pseudosection data

You have the option to save the pseudosection data in a MATLAB “mat” file.

To save the pseudosection data come back to the simulation window, by clicking on the top left “simulation” tab. Then click on “save”. This created the following file

KLB-1_pseudosection.mat

If you close and relaunch the GUI, you can load the saved pseudosection by entering its name in the “Filename” window and click on “load”. Note that loading can potentially take a long time if the pseudosection you saved contains a large number of points

P-X and T-X diagrams

The objective of an P,T-X diagrams is to fix pressure or temperature and vary one or more components of the bulk-rock composition. This section shows how this can be achieved using the GUI of MAGEMin.

Select diagram type

P-X and T-X diagrams can be computed by changing the default option in the top-left corner of the GUI (following snapshot). The fixed pressure can be changed as shown in the bottom-left corner of the following snapshot:

Select compositional range (X)

The compositional range to be explored in a T-X phase diagram can be changed such as:

Here, the TX diagram type is first selected, then the Metapelite database is selected. Using Preset bulk the predefined test 4 has been activated, then Custom bulk is instead selected to enable changing the composition of the bulk. Finally the water-content of the first column (Fraction) is changed to 0.0.
Setting the desired fixed pressure and temperature range, adjusting the number of refinements to 6, and performing the computation results in:

Note that labeling and iso-contouring works in the same way as for PT diagrams.

Save single point output

If one wants to save the exhaustive informations of one computed grid point this can be achieved (after clicking on a grid point) by clicking on Save equilibrium data in the information panel. Doing so opens a window allowing you to save the full output as a text file.

Note that everytime you save the full information about a data point a single calculation is performed and the output format style is the same as for the arg --matlab_out=1

Display iso-contours

Often it is useful to be able to track the lines of constant mineral fraction or end-member proportions. This can be achieved by selecting the Isocontour panel in the bottom-right of the GUI.

Display phase fraction (mode)

To display isocontours of solution phase fraction first enter the acronym of the desired phase, for instance liq in the phase cell. Then select mode and the desired min, range and max values. Finally hitting display isocontour will yield:

Multiple isocontour can be added in a similar manner, and deleted using remove last(s) and remove all buttons.

Display end-member fraction

To display isocontours of the end-member fraction of a solution phase, simply select em frac instead of mode. Doing so will open a side panel from which you can select the end-member list. This gives for liq:

Changing range and color results in:

Save figure (vector)

Computed pahse diagrams including label and isocontour can be saved using the bottom-left Export figure button:

This will save the figure in semi-vectorized format (eps), i.e., that lines labels and contours can be be modified afterward while the colorfield is a bitmap.