Info

• MAGEMinApp.jl Tips

• 1. General setup tab

  • 1.1 General parameters panel

  • 1.2 Contributors panel

  • 1.3 External libraries panel

  • 1.4 Help and contact panel

• 2. Phase diagrams tab

  • 2.1 Setup panel

  • 2.2 Bulk-rock composition panel

  • 2.3 Trace-element composition panel

  • 2.4 General parameters panel

• 3. Diagram sub-tab

  • 3.1 Informations panel

  • 3.2 Display options panel

  • 3.3 Isopleths panel

  • 3.4 Draw path panel

  • 3.5 Uncertainty panel

  • 3.6 Classifications panel

• 4. 3D diagram sub-tab

  • 4.1 Figure and composition bar

  • 4.2 Display panel

  • 4.3 Informations panel

  • 4.4 Field panel

  • 4.5 Surface panel

  • 4.6 Export panel

  • 4.7 Phases and grid panel

• 5. IntersecT sub-tab

  • 5.1 Setup panel

  • 5.2 Results panel

  • 5.3 Options panel

• 6. Trace-elements sub-tab

  • 6.1 REE spectrum panel

  • 6.2 General options panel

  • 6.3 Display options

  • 6.4 TE Isopleths

  • 6.5 Export figure and Phase assemblages panels

• 7. PTX path tab

  • 7.1 Configuration panel

  • 7.2 Bulk-rock composition panel

  • 7.3 Trace Elements panel

  • 7.4 Path definition panel

  • 7.5 Path options panel

  • 7.6 PTX save and export

• 8. General information tab

• Trace-element Kd models

MAGEMinApp.jl Tips

Tip

• Mind that when performing a calculation progress is indicated either by the progress bar at the top right corner of the interface, or by changing the name of your web-browser tab (where MAGEMinApp is opened) to Updating...

• Once a calculation is launched, avoid performing other actions as it may lead to calculation failure

MAGEMinApp.jl interface

The graphic user interface includes 4 main tabs: one for app-wide settings, two for phase equilibrium calculations, and one for supporting reference data.

App-wide settings that apply across every other tab: mineral naming convention, pressure display unit, output directory, plus contributors, third-party libraries and support/contact information.

Available thermodynamic databases are presented here. All other options and parameters are detailed below.

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1. General setup tab

App-wide settings that apply across every other tab.

1.1. General parameters panel

General parameters	Caption
	Mineral names - phase-naming convention used throughout the app: Legacy (MAGEMin's internal codes, e.g. g, ctd, mu) or Warr (2021) (IMA-CNMNC symbols, e.g. Grt, Cld, Ms) Pressure unit - display and input unit for pressure across every tab: kbar or GPa Output directory - folder used for CSV/state exports; edit the path and click Apply to change it (feedback message shown below)

Warning

IntersecT (§5) matches phases between a measurement file and the computed grid using the Warr (2021) symbols. Set Mineral names = Warr (2021) here before using it, otherwise no phase will be found in common.

1.2. Contributors panel

List of people who contributed to MAGEMinApp, together with app/version information.

1.3. External libraries panel

Third-party tools integrated into MAGEMinApp, currently IntersecT (Nerone et al., 2025, doi:10.1016/j.cageo.2025.105949) - an open-source Python package for statistically quantifying the quality of fit in isopleth thermobarometry.

1.4. Help and contact panel

Links for documentation, reporting issues on GitHub, the GitHub repository, and the Discord server.

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2. Phase diagrams tab

2.1. Setup panel

Setup

Caption

General sub-tab Thermodynamic database - select among available thermodynamic databases, grouped as: Published: mp (Metapelite, White et al., 2014), mb (Metabasite, Green et al., 2016), ig (Igneous, Green et al., 2025, after Holland et al., 2018), igd (Igneous, Su et al., 2026, after Tomlinson & Holland, 2021), igad (Igneous alkaline dry, Weller et al., 2024), um (Ultramafic, Evans & Frost, 2021) Mantle: mtl (Mantle, Holland et al., 2013), sb11/sb21/sb24 (Stixrude & Lithgow-Bertelloni, 2011/2021/2024) Custom: ume (Ultramafic extended), mpe (Metapelite extended), mbe (Metabasite extended), all (Global TC dataset - combines every database's oxide set; use Preset below to quickly restrict phases to one database's default set) Dataset - select among available thermodynamic datasets for the chosen database Preset (Global TC dataset only) - quickly restrict the solution-phase selection to match one of the standalone databases (none, Metapelite, Metabasite, Igneous, Igneous alkali-dry, Ultramafic) instead of deselecting phases manually Phase selection - expand to activate or deactivate individual solution and pure phase models Diagram type - P-T, P-X, T-X, PT-X, T-T (polymetamorphic), or P-T-X 3D diagram (pressure × temperature × linear mixing between the two bulk-rock compositions, displayed in the 3D diagram sub-tab) P-T path (PT-X diagram) - table of pressure-temperature points defining the path when Diagram type = PT-X diagram; add rows with "Add new point" or drag-and-drop a P;T CSV file onto "Drag and drop path" to replace the whole path (pressure always given in kbar in the file; see the "Bulk-rock input file" section on the General information tab for the general CSV convention) Solidus H₂O-saturated - saturate the first melt in water at the solidus (true/false) Additional H₂O [mol%] - amount of extra H₂O added when solidus saturation is active (0–100) Buffer - oxygen fugacity buffer or fixed oxide activity: none, QFM, MW, IW, QIF, CCO, HM, NNO, aH₂O, aO₂, aFeO, aMgO, aAl₂O₃, aTiO₂ Latent heat - G0 (no latent heat, default) or G_system (includes the latent heat of reaction); selecting G_system forces Solver to Legacy (see "Latent heat of reaction" in the Phase diagrams tutorials) Clinopyroxene - switch between Omphacite (Omph) and Augite (Aug) for the metabasite database Limit Ca-opx - enforce a maximum Ca content in orthopyroxene (0–1; default 0.5) Pressure [kbar] - minimum and maximum pressure range for the diagram Temperature [°C] - minimum and maximum temperature range for the diagram Fixed pressure / temperature - single pressure or temperature value for P-X and T-X diagram types Initial grid subdivision - sets the starting grid resolution (2–9; default 4, yielding a 16×16 grid) 3D grid [points per axis] (P-T-X 3D diagram only) - number of grid points along P, T and X (default 17 × 17 × 9), with a live estimate of the number of points, computation time and memory. It replaces Initial grid subdivision and the refinement options: 3D diagrams use a regular grid without adaptive refinement. Options that do not apply to 3D diagrams (fixed pressure/temperature, P-T path, solidus H₂O saturation, T-T events, μ-μ and trace-element options) are hidden. Refinement type - refine on phase boundaries (ph) or dominant end-members (em) Refinement levels - number of adaptive mesh refinement levels applied (default 3) Trace elements sub-tab TE predictive model - enable trace-element partitioning at suprasolidus conditions (true/false) Upload Kd's - drag-and-drop zone (or file selection) to load a custom Kd database from an XLSX file Kd's database - Kd database: O. Laurent (2012), J. Cornet (2019, lattice strain) or Yakymchuk et al. (2025) Zr saturation - zircon saturation model: none, Watson & Harrison (1983), Boehnke et al. (2013), Crisp & Berry (2022) P₂O₅ saturation - fluorapatite saturation model: none, Klein et al. (2026), Tollari et al. (2006), Bea et al. (1992, after Harrison & Watson, 1984) S saturation - sulfide saturation model: none, Liu et al. (2007), O'Neill (2021) CO₂ saturation - CO₂ fluid saturation model: none, SY26 (Sun & Yao, 2026) Monazite saturation - monazite saturation model: none, Stepanov et al. (2012), Montel (1993), Maimaiti et al. (2019) EODC - empirical oxide–distribution coefficient model: KP, IL, B, AV; with an associated ratio field (0–1) Seismic properties sub-tab Seismic averaging scheme - averaging scheme for seismic velocities: VRH (Voigt-Reuss-Hill) or HS (Hashin-Shtrikman) Weight factor - mixing weight between Voigt and Reuss bounds (0–1; default 0.5) Seismic correction - apply the melt-content velocity correction (Clark et al., 2017, after Takei, 1997) (true/false). When true, Aspect ratio (melt-pocket aspect ratio), Anelastic correction with its Anelastic model (dry, damp or wet mantle), Shallow correction and Fluid as melt become available Solver sub-tab Solver - Gibbs energy minimization algorithm: Legacy (linear programming, default), PGE (projected gradient) or Hybrid Optimizer - local minimizer of the solution phases, shown only with Solver = Legacy on the THERMOCALC and Stixrude & Lithgow-Bertelloni databases: NLopt or Nullspace (default). With Nullspace, oxides set to exactly 0 in the bulk-rock table are removed from the system, so reduced systems (e.g. CMAS, FeO-free) can be computed; with NLopt they are raised to 1e-4 mol fraction. Also used by the 3D diagram and by the Uncertainty runs (see "Reduced chemical systems" in the Phase diagrams tutorials and "MAGEMin_C.jl: options") Boost mode - use the previous refinement level as an initial guess for the next (true/false) Verbose - level of output in the Julia terminal: none, light or full

2.2. Bulk-rock composition panel

Setup

Caption

System unit - display and input the bulk-rock composition in mol% or wt% Drag and drop - upload a bulk-rock CSV file or drag and drop it onto the dashed upload zone Bulk-rock list - select from pre-defined or previously uploaded bulk-rock compositions for the chosen database; a second list appears for the right-hand composition when Diagram type needs two end-members (P-X, T-X, PT-X) Composition table - editable table showing the loaded oxide composition; values can be modified directly Oxide coverage alert - warns if the selected composition does not cover every oxide required by the currently selected phases (only checked when Database = Global TC dataset (all)) Buffer offset - shift the oxygen fugacity relative to the selected buffer (–50 to +50; default 0)

2.3. Trace-element composition panel

When TE predictive model = true, a third collapsible panel appears below the bulk-rock panel:

Trace-element panel	Caption
	Drag and drop - upload a custom trace-element file (CSV with element and μg/g columns) TE composition list - select from built-in trace-element compositions TE table - editable table showing element concentrations in μg/g (ppm)

2.4. General parameters panel

General parameters

Caption

Title - set the title for the phase diagram; use Update/Reset buttons to apply or revert Compute phase diagram - launch the calculation (green button) Save/Load diagram - save or reload a computed diagram together with all selected options (modal dialogs with filename input) Advanced options - load custom W interaction parameters from a file path Directory window - read-only field showing the folder where exported CSV data will be saved

Note

Contributors, external libraries and help/contact information moved to the top-level 1. General setup tab.

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3. Diagram sub-tab

The Diagram sub-tab has a right-hand sidebar with six tabs: Informations, Display options, Isopleths, Draw path, Uncertainty, and Classifications.

3.1. Informations panel

Informations

Caption

Computation info - read-only summary of the last computed point (phase assemblage, conditions, fractions) Pie unit - unit for the pie chart: mol%, wt%, or vol% Pie chart - shows the modal fractions of stable phases at the selected point Transfer point as bulk - transfer the composition of Solid, Melt, or Whole-rock at the selected point to the bulk-rock composition panel; provide a name and click Transfer Save point - save the full point information to a CSV or text file (`csv file` / `Text` buttons) Save all - save all computed points to a CSV file Export references - export citations for the active models as a BibTeX file Statement of code availability - expandable card; click "Retrieve statement" to display a ready-to-use statement for methods sections (copyable) Display point snippet for MAGEMin_C - expandable card showing the equivalent MAGEMin_C.jl code to reproduce the selected point calculation (copyable)

3.2. Display options panel

Display options

Caption

Field - select the scalar field to display as a color map, e.g.: Hash, Variance, #Phases, G_system, entropy, enthalpy, s_cp, alpha, log10(fO2), log10(dQFM), aH2O, aFeO, aMgO, aAl2O3, aSiO2, aTiO2, melt viscosity (eta_M), ρ_system/ρ_solid/ρ_melt/Δρ, solid and melt mol/wt/vol fractions, Vp, Vs, Vp/Vs, Vp_S, Vs_S, Vp_S/Vs_S, Vp_cor, Vs_cor (seismic-corrected), bulk residual norm, computation time, status. The same field catalog is reused by the Isopleths "Other" type, the Draw path field profile mode, and the PTX path diagram below Show grid - display the adaptive mesh refinement grid (true/false) Minimum field size - minimum number of cells for a field to receive a phase label (0–1024; default 16) Show phase label - show or hide phase assemblage labels Show reaction lines - show or hide phase boundary lines Reaction line style editor - select a solution phase, then set its reaction line style (solid, dot, dash, longdash, dashdot, longdashdot), width (0–10 px, default 0.75), color and label size; Save/Reset/Update apply the changes for that phase Colormap - choose among: blackbody, Blues (default), cividis, Greens, Greys, hot, jet, RdBu, Reds, viridis, YlGnBu, YlOrRd, plus the R.J. Tamblyn set: Pink, Sunset, Dawn, Almeria, Almeria Extended, Almeria Red, Almeria Blue Value range - manual min/max for the color scale Colormap range - slider restricting which portion of the colormap is used (1–9) Set min to white - set the minimum value of the field to white (incompatible with Colormap range) Reverse colormap - invert the colormap direction Smooth colormap - interpolation quality: fast, best, or none

Note

Per-phase stable-color customization ("Modify phase colors") is configured from the PTX path tab (§7) and applies app-wide, not from this panel.

3.3. Isopleths panel

Isopleths

Caption

Isopleth type - Pure phase (pp), Solution phase (ss), or Other (of - system-level field, using the same Field catalog as Display options) Phase - select the phase to contour (solution-phase type) Field (solution-phase type) - Mode, Oxide composition, End-member mode, Mg#, Calculator (oxides), Calculator (apfu), or Calculator (site fractions) Remove excess fluid - exclude fluid from the normalization when computing fractions (true/false) Unit - mol, wt, or vol Custom calculator - enter an expression (e.g., Mg / (Mg + Fe) for apfu, MgO / (MgO + FeO) for oxides) using oxide names, end-member names, or site fractions (available sites are listed above the input for the site-fraction calculator), plus a custom name for the field Range: min / step / max - define the isocontour interval Line style - solid, dot, dash, longdash, dashdot, longdashdot Line width - line thickness in pixels (0–10) Color - color picker for the isocontour lines Label size - font size for isocontour labels (6–20) Add - add the configured isocontour to the diagram Displayed / Hidden lists - manage which isopleths are currently shown or hidden Hide / Hide all / Show / Show all / Remove / Remove all - batch management buttons Export isocontour(s) - export the currently displayed isopleths (requires at least one to be displayed)

3.4. Draw path panel

This panel allows you to manually trace a P-T path directly on the phase diagram by clicking points, then extract the phase or field evolution along it.

Draw path

Caption

Record - toggle on to start recording clicked points on the diagram as path nodes Point counter - displays the number of recorded points Display - what to compute along the path once generated: Phase fractions (stacked area chart) or Field profile (line plot of one field from the Display options catalog, selected via an additional Field dropdown) Clear - remove all recorded points Remove last - delete the most recently added point System unit - unit for the generated path data: mol, wt, or vol (Phase fractions mode) Generate - compute the phase fractions/field values and compositions along the recorded P-T path Path table - read-only table showing the recorded path points (#, P [kbar], T [°C]) Export to PTX path - send the recorded points as the starting path definition of the PTX path tab (§7.4) Phase fractions / field profile plot - chart along the generated path (expandable canvas)

3.5. Uncertainty panel

Recomputes the current P-T phase diagram for many bulk-rock compositions to show how far each phase boundary moves. Two modes are available: Monte Carlo (random sampling), which perturbs the bulk with a 1σ per oxide (Bulk uncertainty table), and Linear between two bulks, which steps along the straight line from the reference bulk to a second bulk (Bulk variation card). The Run card sets the number of realizations (or steps) and launches the run; Display results reopens the result panel (boundary diagram, probability map, bulk spider diagram, SVG export). The status message at the top is shown until a P-T diagram with a fixed bulk composition has been computed. See 17. Bulk-rock uncertainty for a complete walkthrough.

3.6. Classifications panel

Note

Marked "Work in progress" in the app.

Computes and displays TAS and AFM classification diagrams for the melt composition across the computed grid.

Classifications	Caption
	Compute TAS & AFM - compute the classification diagrams for the melt composition at every grid point Display - open the classification canvas (TAS, TAS with volcanic-rock fields, and AFM diagrams)

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4. 3D diagram sub-tab

This sub-tab is only shown when Diagram type = P-T-X 3D diagram is selected in the Setup panel. Clicking Compute phase diagram then computes a regular three-dimensional grid and switches to this sub-tab when the calculation is complete:

• P and T span the pressure and temperature ranges of the Setup panel;

• X is the linear mixing between the two bulk-rock compositions of the Bulk-rock composition panel, labelled X = 0 (left) and X = 1 (right) when this diagram type is selected, as for P-X and T-X diagrams. A message below the tables states what X represents, and warns when both compositions are identical (nothing would vary along X). When only one oxide differs between the two compositions (the others keeping their proportions), e.g. the H₂O content, the X axis of the figure is labelled with that oxide and its content in mol% (a P-T-H₂O diagram);

• the number of points along each axis is set by 3D grid [points per axis] (no adaptive refinement). The progress bar reports the calculation one X plane at a time.

The sub-tab has the figure on the left and, on the right, an always-visible Display panel followed by five tabs: Informations, Field, Surface, Export and Phases & grid.

Tip

• The quantity selectors of the Field and Surface panels follow the same structure as the Isopleths panel of the Diagram sub-tab: Type (Pure phase, Solution phase or Other), Phase, Field (Mode, Oxide composition, Endmember mode, Mg#, Calculator oxides, Calculator apfu, Calculator site fractions; or a system field for Other), and only the options required by the selected field (Unit, Remove excess fluid, Oxide, Endmember, or the calculator expression, with the available site fractions listed for the site-fraction calculator).

• Phase compositions (Mg#, oxides, end-members, calculators) are undefined where the phase is not stable, so the corresponding surfaces stop at the phase stability boundary. Phase modes are zero where the phase is absent.

• The computational cost grows with the number of grid points (roughly 4 ms per point on 12 threads, and ~30 kB of memory per point): 17 × 17 × 9 points take ~10-20 s, 33 × 33 × 33 points a few minutes and ~1 GB of memory.

4.1. Figure and composition bar

Figure

Caption

Composition bar - shows the bulk composition of the last clicked grid node (system acronym and mol% values), with a copy button 3D view - rotate (left click), zoom (scroll) and pan (right click); hovering displays P, T, X and the value of the displayed quantity. The camera icon of the toolbar saves a PNG image Caption - top left, next to the MAGEMin logo: definition of the coloured surface and of its contour lines when this layer is displayed Colorbars - one for the field layer and one for the coloured surface (stacked when both are displayed); legend - phase-in/out surfaces, click an entry to hide/show that surface (double-click to isolate it) Information block - below the figure, as for 2D diagrams: MAGEMin, MAGEMin_C and GUI versions, number of grid points, date and time, database and dataset, solution models, diagram type, meaning of the X axis, solver, oxide list, buffer (if any), X0 and X1 compositions [mol%], pressure and temperature ranges, and computation time

4.2. Display panel

Display

Caption

Layers - any combination of: Field isosurfaces / volume (§4.4), Coloured surface (+ contours) (§4.5), Phase-in/out surfaces and Grid points (assemblage) (§4.7). Ticking a layer opens the tab holding its settings Reverse T axis - reverse the temperature axis (default false) Reverse P axis - reverse the pressure axis (default true) Camera - 3D (perspective), or orthographic views along one axis: P-T (along X), P-X (along T), T-X (along P) Reset view - restore the selected camera after rotating or zooming. Changing any other display option keeps the current view

4.3. Informations panel

Informations

Caption

Clicked point - Nearest grid node (instant, default) or Exact point (computed): a single MAGEMin calculation at the exact P-T-X of the click, with the same database, options and bulk-rock compositions as the diagram (about 1 s). The selected location is marked by a red diamond in the figure and summarized in a status line Pie unit - mol%, wt% or vol% Pie chart - modal fractions of the stable phases at the selected point (click any surface or grid point of the figure); clicking the figure opens this panel automatically Mineral composition - click a slice of the pie chart to display the composition of that phase (oxide, mol%, wt%, apfu), with a copy button

4.4. Field panel

Field

Caption

Quantity - Type / Phase / Field / ... selector (see the tip above), e.g. Other → Melt vol fraction (default), Solution phase → g → Endmember mode → alm, or Solution phase → cpx → Calculator site fractions → xNaM2 / (xNaM2 + xCaM2) Rendering - Isosurfaces or Volume Min value / Max value / Number of surfaces - isosurfaces are drawn at evenly spaced values between min and max. They are reset to the data range when a new quantity is selected; for Variance and number of phases, surfaces are placed at half-integer values with a discrete colour scale Opacity and Show caps (closes the isosurfaces at the box faces) Colormap and Reverse colormap - same colour scales as the Diagram sub-tab

Note

A message is shown above the figure instead of the field when the selected quantity is undefined everywhere (e.g. invalid calculator expression) or constant over the whole diagram (e.g. a pure phase that is never stable).

4.5. Surface panel

The coloured surface reproduces a classic 3D representation: the surface on which a first quantity takes a given value, coloured by a second quantity, with labelled contour lines of a third quantity drawn on it (e.g. the surface of melt Mg# = 0.7, coloured by the melt fraction, with garnet modal contours). Colours and contour values are interpolated on the surface from the surrounding grid nodes where the quantity is defined, so that a surface lying on a phase boundary (e.g. garnet-in) can be coloured by a composition of that phase.

Surface

Caption

Preset (optional) - fills the three blocks below in one go: Melt Mg# = 0.7 (colour: melt fraction, lines: garnet mode), Solidus (melt-in) (colour: H₂O activity, lines: garnet mode), Garnet-in (colour: pyrope in garnet, lines: melt fraction), Density = 3000 kg/m³ (colour: melt fraction, lines: Vp). Every setting can then be modified Surface - the quantity defining the surface (default Solution phase → liq → Mg#), its Value, and the range of that quantity over the diagram Colour of the surface - the quantity used to colour the surface (default melt mode, vol), colormap, reverse colormap and opacity Contour lines on the surface - show contours (true/false), the contoured quantity (default garnet mode, vol), number of levels (evenly spaced over its range on the surface), line width and label size

4.6. Export panel

Export

Caption

File name - base name of the exported files, saved in the output directory (shown at the bottom of the panel) Interactive HTML (shareable, one file) - the current view as a single self-contained HTML file (plotly.js and the logo are embedded, ~5 MB). It opens in any web browser, without MAGEMinApp or an internet connection, and keeps rotation, zoom, hover values, legend, colorbars and information block. Convenient to share a diagram by email or as supplementary material Surfaces: PLY (colour) + STL - one PLY and one STL file per displayed surface (field isosurfaces at the selected levels, coloured surface, phase-in/out surfaces) in a <name>_meshes folder, with a README listing the surfaces. PLY files keep the colours (vertex colours) and open in e.g. Blender, MeshLab or ParaView; STL files contain the geometry only (e.g. for 3D printing) Full grid for ParaView (VTK) - the whole computed grid as a VTK file with ~60 quantities at every node: P [kbar], T [°C] and X, all system fields (density, melt fraction, seismic velocities, activities, ...), the volume mode of every phase, and the quantities currently selected in the Field and Surface panels. In ParaView any isosurface, slice, threshold or volume rendering can then be explored interactively

Note

Mesh and VTK coordinates are normalized to a 0-100 cube in data orientation (x = P, y = T, z = X, all increasing; the axis reversals of the view are not applied), so that the physical units do not distort the shapes and the meshes overlay the VTK grid exactly. The README of the mesh folder and the VTK header give the corresponding P, T and X ranges.

4.7. Phases and grid panel

Phases & grid	Caption
	Phase-in/out surfaces - select the phases whose stability boundary is drawn (isosurface of the phase volume fraction at Threshold, default 0.001), in the phase colour used throughout the app; Opacity Grid points - display every n-th grid node, coloured by variance; hovering shows the stable assemblage. Marker size

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5. IntersecT sub-tab

Implements quantitative isopleth thermobarometry (Nerone et al., 2025, doi:10.1016/j.cageo.2025.105949): for every grid point of a previously computed phase diagram, the modelled a.p.f.u. composition of one or several mineral phases is compared to a measured (e.g. EPMA) composition, returning a goodness-of-fit map.

Warning

Requires Mineral names = Warr (2021) in 1.1 General parameters panel - IntersecT matches phases between the measurement file and the computed grid using Warr (2021) symbols.

The sub-tab is organized in three columns: Setup, Results (Diagrams / Log), and Options.

5.1. Setup panel

Setup

Caption

Run IntersecT - launch the calculation for the currently loaded measurement file and selected phases Keep (accumulate runs for comparison) - when on, every run is stored (up to 8) instead of replacing the previous one; kept runs are listed in the Kept runs tab of the Results panel Measurement file - drag-and-drop a CSV file with measured mineral compositions; the status line reports the loaded file name once parsed Stable phases - checklist automatically populated with the phases found both in the measurement file and on the computed grid; uncheck a phase to exclude it Analysis type - WDS spot, WDS map, or EDS; used to auto-estimate analytical uncertainty when the measurement file does not already provide one Export references - export citations for MAGEMin, the thermodynamic database and IntersecT as a BibTeX file

5.2. Results panel

Results

Caption

Diagrams tab - main "Display" dropdown (populated after Run IntersecT: Qcmp weighted/unweighted, redchi2 total, per-phase and per-element Qcmp/redchi2 fields) and diagram; two smaller "Display" dropdown + diagram pairs below let you compare two more fields side by side Kept runs tab - select one of the stored runs to display its summary, its diagram and its log; Remove selected and Remove all delete stored runs. A warning is shown when the diagram setup of a kept run (database, diagram type, bulk composition, buffer or axes range) differs from that of the previous kept run, since the two runs are then not directly comparable Log tab - full text report: for each selected phase and measured element, the (P,T) location and value of the maximum Qcmp and minimum reduced-χ², the overall weighted/unweighted optimum, and any warnings

5.3. Options panel

Options

Caption

Color options - Colormap (same list as Display options plus RdYlGn, default RdBu), Value range, Colormap range, Set min to white, Reverse colormap, Smooth colormap Overlay options - Show grid, Show phase label, Show reaction lines Isocontours - Type - Measurements (contour a modelled a.p.f.u. field for a Phase/Element pair from the measurement file) or Field (contour one of the IntersecT result fields, available after Run IntersecT) Isocontours - Range / style - Min/Step/Max, Line style, Line width, Color, Label size, then Add Displayed / Hidden lists - manage isocontours (Hide / Hide all / Remove / Remove all, Show / Show all), exactly as in the Isopleths panel

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6. Trace-elements sub-tab

The Trace-elements sub-tab becomes active after a phase diagram has been computed with TE predictive model = true. It displays element distributions and saturation fields across the phase diagram.

6.1. REE spectrum panel

Open by default, above the main diagram.

Rare Earth Elements spectrum	Caption
	Show - ree (rare earth elements only) or all (every predicted trace element) Norm. - normalization reference: bulk or chondrite Spectrum plot - click any suprasolidus grid point to display its trace-element spectrum; double-click a phase in the legend to isolate it

6.2. General options panel

General options	Caption
	Load/Reload trace-elements - (re)load the trace-element prediction for the currently computed diagram Save point - save the TE data at the clicked point to CSV Save all - save TE data for all computed points to CSV Export references - export BibTeX citations for the active Kd and saturation models

6.3. Display options

TE Display options

Caption

Field type - choose the category of field to display: Zircon, Sulfide, Fluorapatite, CO₂ saturation, Trace element Field - specific variable within the selected field type: Zircon: Sat_Zr_liq [ppm], zrc_wt [wt fraction] Sulfide: Sat_S_liq [ppm], sulf_wt [wt fraction] Fluorapatite: Sat_P2O5_liq [ppm], fapt_wt [wt fraction] CO₂ saturation: Sat_CO2_liq [ppm], fl_CO2_wt [wt fraction] Trace element: concentration in the melt via Field builder Field builder (Trace element only) - enter a custom expression using [M_X] for element X in the melt (e.g., [M_Dy] / [M_Yb]); set normalization (none, bulk, chondrite) and click Compute and display Available phases - list of phases for which TE concentrations are available Show reaction lines / Show grid / Show phase label - same diagnostic overlays as the phase-diagram Display options Colormap - same list as 3.2 Display options panel (no RdYlGn); default RdBu Value range - manual color scale min/max Colormap range - slider restricting the colormap portion used Set min to white / Reverse / Smooth - same as in the phase diagram Display options (Reverse colormap defaults to true here)

6.4. TE Isopleths

The Isopleths panel in the Trace-elements sub-tab works identically to the one in the Diagram sub-tab but operates on TE and saturation fields (Zircon, Sulfide, Fluorapatite, CO₂ saturation, Trace element) instead of thermodynamic fields; for the Trace element type it exposes a Calculator expression plus a normalization setting (bulk, chondrite, none) and a custom field name.

6.5. Export figure and Phase assemblages panels

Side panels	Caption
	Export figure - "Export all layers" saves each TE field layer as a separate image file in the output directory Phase assemblages - table of stable phase assemblages on the grid, with a clipboard button and a "Clear" button to reset any highlighted assemblage

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7. PTX path tab

The PTX path tab is divided into a left configuration panel and a central results area. It supports all P-T-X path modes from the same interface, including isentropic paths, which combine with every other mode (fractional melting/crystallization, assimilation, trace elements).

7.1. Configuration panel

Configuration

Caption

Thermodynamic database / Dataset / Preset / Phase selection - same options as the phase diagram Setup panel Clinopyroxene / Limit Ca-opx - same as the phase diagram Setup panel Buffer - same oxygen fugacity buffer / fixed oxide activity list as the phase diagram Setup panel Variable buffer - allow the buffer offset to vary per path point via a Buffer column in the Path definition table (true/false) Solver - pge (projected gradient), lp (Legacy), or hyb (Hybrid); default Legacy Optimizer - NLopt or Nullspace (default); shown only with Solver = Legacy on databases that support it, same as the phase diagram Setup panel Specific Cp - 0: G0 (no latent heat), 1: G_system (with latent heat); selecting G_system forces Solver to Legacy Verbose - none, light, or full Julia terminal output Seismic averaging scheme - VRH (Voigt-Reuss-Hill) or HS (Hashin-Shtrikman) Weight factor - mixing weight between Voigt and Reuss bounds (0–1; default 0.5) Seismic correction - apply melt-content velocity correction (Clark et al., 2017 after Takei, 1997) (true/false) Aspect ratio - melt-pocket aspect ratio used by the seismic correction (0–1; default 0.3; visible when Seismic correction = true) Anelastic correction - apply anelastic attenuation correction (Behn et al., 2009; Cobden et al., 2018) (true/false; visible when Seismic correction = true) Anelastic model - Dry mantle, Damp mantle, or Wet mantle (saturated) attenuation strength (visible when Anelastic correction = true) Shallow correction - fixed-aspect-ratio (0.25), depth-dependent porosity correction for shallow conditions (true/false; visible when Seismic correction = true) Fluid as melt - treat any free fluid phase as melt for the seismic corrections (true/false; visible when Seismic correction = true)

7.2. Bulk-rock composition panel

Same controls as the phase diagram bulk-rock panel (§2.2). When Assimilation = true, a second bulk-rock composition panel appears for the assimilated end-member.

7.3. Trace Elements panel

Appears when TE predictive model = true in Path options.

Trace Elements (PTX)

Caption

KD model - lattice-strain Kd database: OL (O. Laurent, 2012) or CO (J. Cornet, 2019) Zr saturation - none, Watson 1979 (WH), or Blundy 2022 (CB) S saturation - none or Liu 2021 (Liu07) P₂O₅ saturation - none or Tollari 2006 CO₂ saturation - none or SY26 (Sun & Yao, 2026) Upload trace-element file - drag-and-drop a CSV file with element concentrations Initial TE bulk composition [μg/g] - editable table with element concentrations; pre-populate from built-in database dropdown Assimilant TE bulk composition [μg/g] - second TE table for the assimilated end-member (visible when Assimilation = true)

7.4. Path definition panel

Path definition

Caption

P-T path table - pressure-temperature points defining the path (P in kbar or GPa depending on the pressure-unit setting, T in °C); an Add [%] column appears when Assimilation is enabled and a Buffer column when Variable buffer is enabled (§7.5 Path options panel) Add new point - append a new row to the path table Drag and drop path - upload a CSV file to replace the whole path table at once; header P;T (required) plus optional Assim;Buffer columns (default 0.0 if omitted) - pressure always given in kbar in the file, converted to the current display unit Find solidus / Find liquidus - bisection search for the solidus/liquidus temperature at a given pressure, for the current bulk-rock composition Get O at liquidus - adjust the bulk O content so the selected buffer is stable at the liquidus Add phase extraction - opens the "Advanced path definition" panel to cap a mineral's modal proportion along the path: pick a Phase, Unit (mol/wt/vol) and Threshold [%], then Add column; once a step's proportion of that phase exceeds the threshold, only the excess is removed from the bulk carried into the next step. Re-minimize after capping (true/false) controls whether the capped point itself is re-equilibrated with the post-extraction bulk (pinning the displayed proportion at the threshold) or left showing the pre-cap value (default). Configured threshold columns can be removed individually via Remove phase threshold

7.5. Path options panel

Path options

Caption

Resolution - number of calculation steps between two consecutive path points (1–1024; default 32) P-T-X mode - Equilibrium, Fractional melting, or Fractional crystallization Assimilation - enable progressive addition of a second bulk-rock composition (true/false) TE predictive model - enable trace-element partitioning along the path (true/false) Cumulate/Connectivity unit - basis (mol, wt, or vol) used for the assimilation blend and the melt/solid extraction mass balance; only shown in fractional melting/crystallization mode Connectivity threshold [mol%] - melt fraction above which melt is extracted during fractional melting (0–100; default 7); only visible in fractional melting mode Residual Threshold [mol%] - melt fraction left in the rock after an extraction event (0 to the connectivity threshold; default 7, i.e. melt is brought back to the connectivity threshold). A lower value drains the melt further each time the connectivity threshold is exceeded; the value is clamped to the connectivity threshold. Only visible in fractional melting mode Residual rock fraction [mol%] - fraction of solid entrained by the fractionating melt during fractional crystallization (0–100; default 0); only visible in fractional crystallization mode Isentropic - compute an isentropic (constant-entropy) path (true/false). The path table then only holds the pressures (plus Add [mol%] when Assimilation is on); the temperature is a single Starting Temp. [°C] field above the table, and the temperature at each following pressure is found by bisection (Tolerance [K]) so that the entropy of the system equals the starting entropy. The Path preview panel shows the resulting P-T path and the Starting entropy [kJ/K] Solidus H₂O-saturated - saturate the first melt in water at the solidus (true/false) Additional H₂O [mol%] - extra H₂O added at water saturation (visible when Solidus H₂O-saturated = true) Compute path - launch the P-T-X path calculation (green button)

7.6. PTX save and export

All export options are located in the Path options panel:

Button	Content
Save path → csv	Full path: P, T, phase fractions and compositions at each step
Save path → csv line	Same but all steps on a single row
Save cumulate → csv file	Composition of the cumulate (extracted solid) at each step
Save trace elements → csv file	TE concentrations in melt, solid and minerals at each step (requires TE computation)
Save cumulate TE → csv file	Integrated cumulate TE composition at each step (requires TE computation)
Export references → bibtex file	BibTeX citations for active models and database

Note

• The Save trace elements and Save cumulate TE buttons are only active after trace elements have been computed.

• The export path is printed in the Julia terminal.

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8. General information tab

Provides static reference data across three sections:

• Solution phases table - full mineral name, abbreviation, Warr (2021) symbol and solvus daughters, for every solution phase of every database (short and citation-tagged names alike), sorted alphabetically; - marks a phase with no Warr equivalent or no solvus (filterable, 16 rows per page)

• End-members table - full mineral name, abbreviation, Warr (2021) symbol and composition in the 15-oxide basis of the global database, sorted alphabetically (filterable, 16 rows per page)

• CSV bulk-rock format - example table showing the required column structure for bulk-rock input files (title, comments, db, sysUnit, oxide columns, optional _frac2 variants), followed by the full field documentation including the thermodynamic dataset acronym table (mtl, mp, mb, ig, igd, igad, um, sb11, sb21, sb24, ume, mpe, mbe, all)

• Trace-element Kd tables - three tabs subdivided by SiO₂ content of the melt (SiO2 < 52 wt%, 52 wt% <= SiO2 < 63 wt%, 63 wt% <= SiO2); each shows the element × mineral Kd matrix (filterable, 32 rows per page)

• Calculation details - static reference cards describing phase deactivation logic, oxide activity formulation, water saturation methodology, specific heat capacity calculation, the site fraction calculator, and seismic velocity corrections (melt/anelastic/shallow, cross-referencing the PTX path Configuration panel controls)

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Note

Trace-element partitioning model descriptions and Kd tables are documented in the Thermodynamic Databases page.