burnman-cpp 0.17.0__tar.gz → 0.21.0__tar.gz

{burnman_cpp-0.17.0 → burnman_cpp-0.21.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: burnman_cpp
-Version: 0.17.0
+Version: 0.21.0
 Summary: Python bindings for the BurnMan C++ mineral physics library
 Author-Email: The BurnMan Team <bob.myhill@bristol.ac.uk>
 License-Expression: GPL-3.0-or-later
@@ -20,10 +20,12 @@ Provides-Extra: test
 Requires-Dist: pytest>=7; extra == "test"
 Requires-Dist: sympy>=1.10; extra == "test"
 Requires-Dist: matplotlib>=3.6; extra == "test"
+Requires-Dist: shapely>=2.0; extra == "test"
 Provides-Extra: symbolic
 Requires-Dist: sympy>=1.10; extra == "symbolic"
 Provides-Extra: examples
 Requires-Dist: matplotlib>=3.6; extra == "examples"
+Requires-Dist: shapely>=2.0; extra == "examples"
 Provides-Extra: contrib
 Requires-Dist: matplotlib>=3.6; extra == "contrib"
 Requires-Dist: pandas>=1.5; extra == "contrib"
@@ -152,6 +154,8 @@ Optional Python dependencies are installed through extras:
 - **pytest 7 or newer** (`test`): runs the Python test suite.
 - **Matplotlib 3.6 or newer** (`examples`): plots examples, phase diagrams and
   diagnostic figures; it is also needed by the plotting tests.
+- **Shapely 2.0 or newer** (`examples`): clips interpolated composition contours
+  to phase-field boundaries and holes; it is also included in the test extra.
 - **Python BurnMan 2.1 or newer** (`reference`): enables adapters and comparisons
   with the original implementation. The reference tests below use a specific
   Git commit for reproducibility.

{burnman_cpp-0.17.0 → burnman_cpp-0.21.0}/README.md

@@ -115,6 +115,8 @@ Optional Python dependencies are installed through extras:
 - **pytest 7 or newer** (`test`): runs the Python test suite.
 - **Matplotlib 3.6 or newer** (`examples`): plots examples, phase diagrams and
   diagnostic figures; it is also needed by the plotting tests.
+- **Shapely 2.0 or newer** (`examples`): clips interpolated composition contours
+  to phase-field boundaries and holes; it is also included in the test extra.
 - **Python BurnMan 2.1 or newer** (`reference`): enables adapters and comparisons
   with the original implementation. The reference tests below use a specific
   Git commit for reproducibility.

burnman_cpp-0.21.0/examples/data/input_compositions/SOURCES.md

@@ -0,0 +1,11 @@
+`dhz_mineral_compositions.dat` is copied unchanged from Python BurnMan's
+`burnman/data/input_compositions` directory for `example_composition.py`.
+The reference revision is recorded in
+[the reference policy](../../../tests/reference/burnman.json).
+
+The table contains oxide weight proportions, oxygen normalization counts,
+mineral names and reference labels for forsterite, pyrope and cummingtonite.
+The original header, values and comments are retained.
+
+BurnMan is distributed under GPL v2 or later; this copy is distributed as part
+of burnman_cpp under GPL-3.0-or-later (see the root LICENSE).

burnman_cpp-0.21.0/examples/data/input_compositions/dhz_mineral_compositions.dat

@@ -0,0 +1,5 @@
+SiO2	TiO2	Al2O3	Cr2O3	Fe2O3	FeO	MnO	MgO	CaO	Na2O	K2O	H2O	Comment
+41.85	0.07	0.00	0.00	0.00	2.05	0.21	56.17	0.00	0.00	0.00	0.00	4 Forsterite p7,1
+41.33	0.28	21.83	1.73	1.44	9.00	0.44	19.60	4.40	0.00	0.00	0.00	24 Pyrope p34,1
+55.57	0.18	0.89	0.00	0.06	17.48	0.45	21.85	1.29	0.13	0.01	2.07	24 Cummingtonite p228,3
+# Lines beginning with hashes (like this one) are not read

burnman_cpp-0.21.0/examples/data/input_seismic/SOURCES.md

@@ -0,0 +1,11 @@
+`ak135_lowermantle.txt` is copied unchanged from Python BurnMan's
+`burnman/data/input_seismic` directory for `example_seismic.py`.
+The reference revision is recorded in
+[the reference policy](../../../tests/reference/burnman.json).
+
+The table is labelled AK135, Kennett et al. (1995). The example reads radius,
+pressure, density and P/S-wave velocities, reversing the rows to increasing depth.
+All original values and comments are retained.
+
+BurnMan is distributed under GPL v2 or later; this copy is distributed as part
+of burnman_cpp under GPL-3.0-or-later (see the root LICENSE).

burnman_cpp-0.21.0/examples/data/input_seismic/ak135_lowermantle.txt

@@ -0,0 +1,47 @@
+# AK135 Kennett et al. (1995)
+# Radius (km) Pressure (Pa), rho (g/m^3) Vp (m/s) Vs (m/s) Qk  Qm
+3.531670e+06 1.328487e+11 5.745800e+03 1.365700e+04 7.270000e+03 7.251100e+02 2.739700e+02
+3.581330e+06 1.299396e+11 5.719600e+03 1.365330e+04 7.259300e+03 7.268700e+02 2.739700e+02
+3.631000e+06 1.270629e+11 5.693400e+03 1.364980e+04 7.248500e+03 7.227300e+02 2.717400e+02
+3.631000e+06 1.270629e+11 5.438700e+03 1.364980e+04 7.248500e+03 9.332100e+02 3.508800e+02
+3.681000e+06 1.241996e+11 5.417600e+03 1.358990e+04 7.225300e+03 9.408800e+02 3.546100e+02
+3.731000e+06 1.213653e+11 5.396200e+03 1.353110e+04 7.203100e+03 9.520000e+02 3.597100e+02
+3.779500e+06 1.186355e+11 5.374800e+03 1.347410e+04 7.180400e+03 9.603600e+02 3.636400e+02
+3.829000e+06 1.158850e+11 5.353100e+03 1.341560e+04 7.158400e+03 9.684600e+02 3.676500e+02
+3.878500e+06 1.131476e+11 5.331300e+03 1.335840e+04 7.136800e+03 9.768100e+02 3.717500e+02
+3.928000e+06 1.104332e+11 5.309200e+03 1.330170e+04 7.114400e+03 9.856300e+02 3.759400e+02
+3.977500e+06 1.077462e+11 5.287000e+03 1.324650e+04 7.093200e+03 9.907700e+02 3.787900e+02
+4.027000e+06 1.050762e+11 5.264600e+03 1.318950e+04 7.072200e+03 9.994400e+02 3.831400e+02
+4.076500e+06 1.024252e+11 5.242000e+03 1.313370e+04 7.050400e+03 1.008790e+03 3.876000e+02
+4.126000e+06 9.979395e+10 5.219200e+03 1.307860e+04 7.028600e+03 1.018380e+03 3.921600e+02
+4.175500e+06 9.718910e+10 5.196300e+03 1.302260e+04 7.006900e+03 1.032140e+03 3.984100e+02
+4.225000e+06 9.459652e+10 5.173200e+03 1.296630e+04 6.985200e+03 1.042070e+03 4.032300e+02
+4.274500e+06 9.201772e+10 5.149900e+03 1.290930e+04 6.962500e+03 1.048090e+03 4.065000e+02
+4.324000e+06 8.946381e+10 5.126400e+03 1.285240e+04 6.941600e+03 1.058030e+03 4.115200e+02
+4.373500e+06 8.692114e+10 5.102700e+03 1.279560e+04 6.919400e+03 1.064230e+03 4.149400e+02
+4.423000e+06 8.439595e+10 5.078900e+03 1.273840e+04 6.897200e+03 1.070380e+03 4.184100e+02
+4.472500e+06 8.188936e+10 5.054800e+03 1.268070e+04 6.874300e+03 1.085970e+03 4.255300e+02
+4.522000e+06 7.939284e+10 5.030600e+03 1.262260e+04 6.851700e+03 1.097160e+03 4.310300e+02
+4.571500e+06 7.691631e+10 5.006200e+03 1.256380e+04 6.828900e+03 1.108580e+03 4.366800e+02
+4.621000e+06 7.444450e+10 4.981700e+03 1.250300e+04 6.805600e+03 1.120090e+03 4.424800e+02
+4.670500e+06 7.199670e+10 4.957000e+03 1.244270e+04 6.782000e+03 1.127020e+03 4.464300e+02
+4.720000e+06 6.955890e+10 4.932100e+03 1.238130e+04 6.757900e+03 1.134010e+03 4.504500e+02
+4.769500e+06 6.713183e+10 4.906900e+03 1.231810e+04 6.732300e+03 1.141320e+03 4.545500e+02
+4.819000e+06 6.472272e+10 4.881700e+03 1.225580e+04 6.707000e+03 1.148760e+03 4.587200e+02
+4.868500e+06 6.232361e+10 4.856200e+03 1.219120e+04 6.681300e+03 1.156040e+03 4.629600e+02
+4.918000e+06 5.994136e+10 4.830700e+03 1.212470e+04 6.655400e+03 1.163160e+03 4.672900e+02
+4.967500e+06 5.757095e+10 4.805000e+03 1.205710e+04 6.628500e+03 1.170530e+03 4.717000e+02
+5.017000e+06 5.521051e+10 4.779000e+03 1.198910e+04 6.600900e+03 1.178190e+03 4.761900e+02
+5.066500e+06 5.287008e+10 4.752800e+03 1.192080e+04 6.572800e+03 1.186060e+03 4.807700e+02
+5.116000e+06 5.053131e+10 4.726600e+03 1.184910e+04 6.543100e+03 1.193990e+03 4.854400e+02
+5.165500e+06 4.820994e+10 4.700100e+03 1.177680e+04 6.513100e+03 1.202040e+03 4.902000e+02
+5.215000e+06 4.590692e+10 4.673500e+03 1.170200e+04 6.482200e+03 1.210020e+03 4.950500e+02
+5.264500e+06 4.361388e+10 4.646700e+03 1.162650e+04 6.451400e+03 1.217910e+03 5.000000e+02
+5.314000e+06 4.133083e+10 4.619800e+03 1.154930e+04 6.418200e+03 1.226520e+03 5.050500e+02
+5.363500e+06 3.906293e+10 4.592600e+03 1.147040e+04 6.386000e+03 1.234540e+03 5.102000e+02
+5.413000e+06 3.680860e+10 4.565400e+03 1.138970e+04 6.351900e+03 1.243020e+03 5.154600e+02
+5.462500e+06 3.456427e+10 4.516200e+03 1.130680e+04 6.316400e+03 1.251690e+03 5.208300e+02
+5.512000e+06 3.233116e+10 4.465000e+03 1.122280e+04 6.279900e+03 1.260680e+03 5.263200e+02
+5.561500e+06 3.011548e+10 4.411800e+03 1.113550e+04 6.242400e+03 1.269440e+03 5.319100e+02
+5.611000e+06 2.791209e+10 4.356500e+03 1.105530e+04 6.210000e+03 1.277930e+03 5.376300e+02
+5.661000e+06 2.569653e+10 4.298600e+03 1.092220e+04 6.089800e+03 1.311170e+03 5.434800e+02

burnman_cpp-0.17.0/examples/green2025.py → burnman_cpp-0.21.0/examples/driver_green2025.py

@@ -11,10 +11,11 @@
 #
 # ------------------------------------------------------
 
-"""Shared runner for Supplement 3 of Green et al. (2025), egae079.
+"""
+Shared driver to recreate the figures in
+Supplement 3 of Green et al. (2025), https://doi.org/10.1093/petrology/egae079.
 
-Use the separate example_green2025_*.py scripts. Thermodynamics, equilibrium,
-boundary tracing and polygon construction use the standard C++ routines.
+Use the separate example_green2025_*.py scripts to make the plots.
 """
 
 from collections import Counter
@@ -23,11 +24,9 @@ from pathlib import Path
 import time
 
 import burnman_cpp as bm
-from burnman_cpp.minerals import HPx_ds636, model_sets
+from burnman_cpp.minerals import model_sets
 from burnman_cpp.tools.phase_diagram_helpers import (
-    example_parser,
-    refine_saved,
-    run_phase_diagram_example,
+    write_phase_diagram,
     save_figure,
 )
 
@@ -36,10 +35,11 @@ SOURCE = "https://doi.org/10.1093/petrology/egae079"
 
 def candidate_phases(composition):
     models = model_sets.igneous("G25")
-    # Match MAGEMin's igneous phase exclusions when H2O is absent, including
-    # the formal dry corners of biotite, cordierite and aqueous fluid.
+    # Exclude nominally hydrous phases when H2O is absent, including
+    # the dry endmembers of biotite, cordierite and aqueous fluid,
+    # which are presumably metastable anyway. Also exclude cor.
     hydrous = {"fluid", "hb", "bi", "ms", "ep", "cd"}
-    phases = [
+    return [
         phase
         for phase in models.phases
         if phase.name != "cor"
@@ -47,18 +47,11 @@ def candidate_phases(composition):
             phase.name not in hydrous or composition.atomic_composition.get("H", 0) > 0
         )
     ]
-    # The reference igneous catalogue includes stishovite, not corundum.
-    stishovite = HPx_ds636.stv()
-    stishovite.set_name("stv")
-    return phases + [stishovite]
 
 
 def compare(composition, reference_points, settings):
-    """Check assemblages at points read well inside the published fields.
-
-    The PDF distinguishes pl/afs, augite/pigeonite and spl/mgt/cm/usp by
-    composition. These are instances of fsp, cpx and sp respectively here.
-    Repeated names preserve coexistence across a solvus.
+    """
+    Check assemblages at points inside the fields reported in the PDF.
     """
     rows = []
     phases = candidate_phases(composition)
@@ -93,7 +86,7 @@ def compare(composition, reference_points, settings):
 
 
 def compare_liquidus(data, pressure_kbar, reference_temperature):
-    """Intersect saved phase lines with the PDF's liquidus comparison isobar."""
+    """Check saved phase lines against the PDF."""
     report = dict(
         pressure_kbar=pressure_kbar,
         reference_temperature_C=reference_temperature,
@@ -163,6 +156,8 @@ def plot(data, target, temperature_range, pressure_range, title, fontsize):
     bm.plot_phase_diagram(
         data,
         ax=ax,
+        pressure_unit="kbar",
+        temperature_unit="C",
         cmap="Blues_r",
         fill_alpha=1.0,
         label_fontsize=fontsize,
@@ -191,105 +186,72 @@ def main(
     pressure_range,
     reference_points,
     liquidus,
+    *,
+    seeds=7,
+    check_only=False,
 ):
-    parser = example_parser(
-        f"Green et al. (2025), Figure S3-{figure}: {title}",
-        Path(__file__).parent / f"green2025_{name}_output",
-        seeds=7,
-        replot=True,
-        refine=True,
-    )
-    parser.add_argument(
-        "--check-only",
-        action="store_true",
-        help="Only compare interior assemblages with the PDF.",
-    )
-    args = parser.parse_args()
-    # These are oxide moles (including atomic O), not oxide weight percentages.
-    # Normalising the amount improves numerical scaling without changing the bulk.
+    output_dir = Path(__file__).resolve().parent / f"green2025_{name}_output"
+    output_dir.mkdir(parents=True, exist_ok=True)
+    # Green et al. (2025) report compositions in oxide molar fractions,
+    # (including atomic O), but the phase diagram code expects atomic fractions.
     composition = bm.Composition(
         {oxide: amount / sum(oxides.values()) for oxide, amount in oxides.items()},
         unit_type="molar",
     )
     settings = bm.PhaseDiagramSettings()
-    settings.pressure_seeds = settings.temperature_seeds = (
-        3 if args.quick else args.seeds
-    )
-    settings.step = 0.035 if args.quick else 0.015
-    settings.max_recovery_passes = 0 if args.quick else 2
-    settings.verbose = args.verbose
-    args.output_dir.mkdir(parents=True, exist_ok=True)
-    started = time.monotonic()
-    if not args.check_only:
-
-        def calculate_section(source=None, verbose=False):
-            phases = candidate_phases(composition)
-            result = (
-                refine_saved(
-                    source,
-                    phases,
-                    composition=composition.atomic_composition,
-                    settings=settings,
-                    verbose=verbose,
-                )
-                if source is not None
-                else bm.phase_diagram(
-                    composition.atomic_composition,
-                    phases,
-                    (max(1.0e5, pressure_range[0] * 1.0e8), pressure_range[1] * 1.0e8),
-                    tuple(t + 273.15 for t in temperature_range),
-                    settings,
-                )
-            )
-            data = result.to_dict()
-            data.update(
-                source=SOURCE,
-                reference_figure=f"S3-{figure}",
-                oxide_molar_amounts=oxides,
-                model_set=model_sets.igneous("G25").to_dict(),
-                calculation_seconds=time.monotonic() - started,
-            )
-            return data
-
-        data = run_phase_diagram_example(
-            parser,
-            lambda options: calculate_section(),
-            args=args,
-            stem=name,
-            refine=calculate_section,
-            plot=lambda result, target, fontsize: plot(
-                result,
-                target,
-                temperature_range,
-                pressure_range,
-                title,
-                fontsize,
-            ),
+    settings.pressure_seeds = settings.temperature_seeds = seeds
+    settings.step = 0.015
+    settings.max_recovery_passes = 2
+    settings.verbose = True
+    if not check_only:
+        started = time.monotonic()
+        result = bm.phase_diagram(
+            composition.atomic_composition,
+            candidate_phases(composition),
+            (max(1.0e5, pressure_range[0] * 1.0e8), pressure_range[1] * 1.0e8),
+            tuple(t + 273.15 for t in temperature_range),
+            settings,
         )
-    if not args.plot_json:
-        rows = compare(composition, reference_points, settings)
-        report = dict(source=SOURCE, figure=f"S3-{figure}", interior_assemblages=rows)
-        if not args.check_only:
-            report["liquidus"] = compare_liquidus(data, *liquidus)
-            report["resolved"] = data["resolved"]
-            report["diagnostics"] = data["diagnostics"]
-            geometry = bm.phase_diagram_field_polygons(data)
-            report["geometry"] = dict(
-                fields=len(geometry.polygons),
-                open_fields=sum(p.has_open_boundary for p in geometry.polygons),
-                unidentified_fields=sum(not p.phases for p in geometry.polygons),
-                covered_area_fraction=sum(p.area for p in geometry.polygons),
-                diagnostics=list(geometry.diagnostics),
-            )
-            print(f"Liquidus comparison: {report['liquidus']}", flush=True)
-        (args.output_dir / f"{name}_comparison.json").write_text(
-            json.dumps(report, indent=2, allow_nan=False)
+        data = result.to_dict() | dict(
+            source=SOURCE,
+            reference_figure=f"S3-{figure}",
+            oxide_molar_amounts=oxides,
+            model_set=model_sets.igneous("G25").to_dict(),
+            calculation_seconds=time.monotonic() - started,
         )
-        print(
-            f"PDF interior assemblages: {sum(row['match'] for row in rows)}/{len(rows)} match.",
-            flush=True,
+        write_phase_diagram(data, output_dir / name)
+        plot(
+            data,
+            output_dir / f"{name}.png",
+            temperature_range,
+            pressure_range,
+            title,
+            7.0,
         )
-        if not all(row["match"] for row in rows):
-            raise RuntimeError(
-                "Assemblages differ from the PDF; see the comparison JSON."
-            )
+
+    rows = compare(composition, reference_points, settings)
+    report = dict(source=SOURCE, figure=f"S3-{figure}", interior_assemblages=rows)
+    if not check_only:
+        report.update(
+            liquidus=compare_liquidus(data, *liquidus),
+            resolved=data["resolved"],
+            diagnostics=data["diagnostics"],
+        )
+        geometry = bm.phase_diagram_field_polygons(data)
+        report["geometry"] = dict(
+            fields=len(geometry.polygons),
+            open_fields=sum(p.has_open_boundary for p in geometry.polygons),
+            unidentified_fields=sum(not p.phases for p in geometry.polygons),
+            covered_area_fraction=sum(p.area for p in geometry.polygons),
+            diagnostics=list(geometry.diagnostics),
+        )
+        print(f"Liquidus comparison: {report['liquidus']}", flush=True)
+    (output_dir / f"{name}_comparison.json").write_text(
+        json.dumps(report, indent=2, allow_nan=False) + "\n"
+    )
+    print(
+        f"PDF interior assemblages: {sum(row['match'] for row in rows)}/{len(rows)} match.",
+        flush=True,
+    )
+    if not all(row["match"] for row in rows):
+        raise RuntimeError("Assemblages differ from the PDF; see the comparison JSON.")

{burnman_cpp-0.17.0 → burnman_cpp-0.21.0}/examples/example_anisotropic_mineral.py

@@ -1,9 +1,20 @@
-# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for
-# the Earth and Planetary Sciences
+# ------------------------------------------------------
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+#
+# SPDX-FileCopyrightText: Copyright (C) 2025-2026 by the BurnMan Team.
+#
+# This file is part of BurnMan.
+#
+# Detailed license information governing the source code
+# and contributions can be found in the LICENSE document.
+#
+# ------------------------------------------------------
+
+# Original example attribution:
 # Copyright (C) 2012 - 2021 by the BurnMan team, released under the GNU
 # GPL v2 or later.
 
-
 """
 example_anisotropic_mineral
 ---------------------------

{burnman_cpp-0.17.0 → burnman_cpp-0.21.0}/examples/example_anisotropy.py

@@ -1,8 +1,20 @@
-# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for the Earth and Planetary Sciences
+# ------------------------------------------------------
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+#
+# SPDX-FileCopyrightText: Copyright (C) 2025-2026 by the BurnMan Team.
+#
+# This file is part of BurnMan.
+#
+# Detailed license information governing the source code
+# and contributions can be found in the LICENSE document.
+#
+# ------------------------------------------------------
+
+# Original example attribution:
 # Copyright (C) 2012 - 2017 by the BurnMan team, released under the GNU
 # GPL v2 or later.
 
-
 """
 example_anisotropy
 ------------------
@@ -228,8 +240,8 @@ if __name__ == "__main__":
             cbar.add_lines(lines)
 
         fig.set_layout_engine("tight")
-        Path("output_figures").mkdir(exist_ok=True)
-        plt.savefig("output_figures/example_anisotropy.png")
+        Path("anisotropy_output").mkdir(exist_ok=True)
+        plt.savefig("anisotropy_output/example_anisotropy.png")
         plt.show()
 
     plot_anisotropic_seismic_properties(talc)

{burnman_cpp-0.17.0 → burnman_cpp-0.21.0}/examples/example_assemblage_relaxation.py

@@ -1,5 +1,17 @@
-# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit
-# for the Earth and Planetary Sciences
+# ------------------------------------------------------
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+#
+# SPDX-FileCopyrightText: Copyright (C) 2025-2026 by the BurnMan Team.
+#
+# This file is part of BurnMan.
+#
+# Detailed license information governing the source code
+# and contributions can be found in the LICENSE document.
+#
+# ------------------------------------------------------
+
+# Original example attribution:
 # Copyright (C) 2012 - 2025 by the BurnMan team, released under the GNU
 # GPL v2 or later.
 
@@ -7,13 +19,6 @@
 example_assemblage_relaxation
 -----------------------------
 
-Adapted from Python BurnMan's example_assemblage_relaxation.py. All materials,
-equilibrium solves and relaxed derivatives use the native C++ implementation;
-the Python BurnMan package is not required.
-
-Run with ``python examples/example_assemblage_relaxation.py`` after installing
-``pip install -e '.[examples]'``.
-
 In this example, we demonstrate how to use the `RelaxedComposite` class
 to compute the properties of a mineral assemblage allowing for
 different levels of compositional and phase relaxation.
@@ -46,7 +51,7 @@ properties of mineral assemblages, which is important for:
 """
 
 import numpy as np
-import burnman_cpp as bm
+import burnman_cpp
 import matplotlib.pyplot as plt
 
 from burnman_cpp import equilibrate
@@ -54,18 +59,6 @@ from burnman_cpp.minerals import SLB_2011
 from burnman_cpp import Assemblage, RelaxedComposite
 from burnman_cpp.tools.chemistry import reaction_matrix_as_strings
 
-
-def solve(composition, assemblage, constraints):
-    # Physical-unit equivalents of the Python example's default tolerances.
-    tolerances = np.r_[1.0, 1.0e-6, np.full(assemblage.n_endmembers, 1.0e-9)]
-    result = equilibrate(composition, assemblage, constraints, tol=tolerances)
-    solutions = result.sol_array.ravel()
-    for solution in solutions:
-        if not solution.success:
-            raise RuntimeError(solution.message)
-    return solutions, result.prm
-
-
 if __name__ == "__main__":
     # Initialize the minerals we will use in this example.
     ol = SLB_2011.mg_fe_olivine()
@@ -79,35 +72,36 @@ if __name__ == "__main__":
     # Find the wad-in and ol-in pressures at 1600 K
     T = 1600.0
     composition = assemblage.formula.copy()
-    prm = bm.get_equilibration_parameters(assemblage, composition)
+    prm = burnman_cpp.get_equilibration_parameters(assemblage, composition)
     equality_constraints = [
-        bm.TemperatureConstraint(T),
-        bm.PhaseFractionConstraint(1, 0.0, prm),
+        burnman_cpp.TemperatureConstraint(T),
+        burnman_cpp.PhaseFractionConstraint(1, 0.0, prm),
     ]
-    solve(composition, assemblage, equality_constraints)
+    equilibrate(composition, assemblage, equality_constraints)
     P_wad_in = assemblage.pressure
 
     equality_constraints = [
-        bm.TemperatureConstraint(T),
-        bm.PhaseFractionConstraint(0, 0.0, prm),
+        burnman_cpp.TemperatureConstraint(T),
+        burnman_cpp.PhaseFractionConstraint(0, 0.0, prm),
     ]
-    solve(composition, assemblage, equality_constraints)
+    equilibrate(composition, assemblage, equality_constraints)
     P_ol_in = assemblage.pressure
 
     # Now get the unrelaxed properties over the two phase region
     # at their equilibrated states
     pressures = np.linspace(P_wad_in + 1.0, P_ol_in - 1.0, 101)
     equality_constraints = [
-        [bm.PressureConstraint(p) for p in pressures],
-        bm.TemperatureConstraint(T),
+        [burnman_cpp.PressureConstraint(P) for P in pressures],
+        burnman_cpp.TemperatureConstraint(T),
     ]
 
-    sols, prm = solve(composition, assemblage, equality_constraints)
-    # Native equilibrium results store parameter vectors, so restore each state
-    # to read its frozen properties (Python BurnMan stores assemblage snapshots).
+    result = equilibrate(composition, assemblage, equality_constraints)
+    sols, prm = result.sol_array.ravel(), result.prm
+    # Native results contain parameter vectors, so restore each state to read
+    # its unrelaxed properties.
     unrelaxed = []
     for sol in sols:
-        bm.set_composition_and_state_from_parameters(assemblage, sol.x)
+        burnman_cpp.set_composition_and_state_from_parameters(assemblage, sol.x)
         unrelaxed.append(
             [
                 assemblage.isentropic_bulk_modulus_reuss,

{burnman_cpp-0.17.0 → burnman_cpp-0.21.0}/examples/example_basalt_phase_diagram.py

@@ -12,32 +12,37 @@
 #
 # ------------------------------------------------------
 
-"""Closed-system basalt phase diagram, 300–900 °C and 0–20 kbar.
-
-All thermodynamics, Gibbs minimisation, phase selection, equilibrium solves
-and boundary continuation run in C++. Python specifies the model/bulk and
-writes JSON and a figure. No Python BurnMan or optimisation library is needed.
-
-The matched HPx metabasite set reproduces the 30 January 2022 THERMOCALC
-calibration: Green et al. (2016) solids and tonalitic melt, HP dataset 6.2,
-and PS94 H2O with the Holland-Powell thermal reference. The model set is
-available as burnman_cpp.minerals.model_sets.metabasite().
-The closed bulk contains exactly 2 wt% H2O; no water/oxygen buffers are used.
-A 1 bar lower calculation limit avoids the fluid singularity at P=0; the
-figure uses the requested 0–20 kbar axis. Increase --seeds to check discovery
-of narrow or disconnected fields. Failed calculations remain explicit.
 """
+Calculate and plot a phase diagram for a basalt composition,
+between 300-900 °C and 0-20 kbar.
+
+This example uses the HPx metabasite set
+from the 30 January 2022 THERMOCALC calibration:
+Green et al. (2016) solids and tonalitic melt, HP dataset 6.2,
+and Pitzer and Sterner (1994)
+H2O with the Holland-Powell thermal reference.
+
+The model set is available as
+burnman_cpp.minerals.model_sets.metabasite().
+The bulk composition contains exactly 2 wt% H2O.
+"""
+
+from pathlib import Path
 
 import burnman_cpp as bm
 from burnman_cpp.minerals import model_sets
 from burnman_cpp.tools.phase_diagram_helpers import (
-    example_parser,
     plot_phase_diagram_example,
     refine_saved,
-    run_phase_diagram_example,
+    write_phase_diagram,
 )
 
+OUTPUT_DIR = Path(__file__).resolve().with_name("basalt_phase_diagram_output")
+SEEDS = 7
+
+
 MODEL_SET = model_sets.metabasite()
+PHASES = MODEL_SET.phases
 
 # Masses in a 100 g wet rock; the sum is 100, including exactly 2 g of H2O.
 BASALT_OXIDES = dict(
@@ -57,25 +62,20 @@ BASALT_COMPOSITION = bm.Composition(
 )
 
 
-def candidate_phases():
-    return model_sets.metabasite().phases
-
-
 def calculate(
     seeds=7,
-    quick=False,
     verbose=False,
     *,
     pressure_range=(1.0e5, 2.0e9),
     temperature_range=(573.15, 1173.15),
 ):
     settings = bm.PhaseDiagramSettings()
-    settings.pressure_seeds = settings.temperature_seeds = 4 if quick else seeds
-    settings.step = 0.04 if quick else 0.025
+    settings.pressure_seeds = settings.temperature_seeds = seeds
+    settings.step = 0.025
     settings.verbose = verbose
     return bm.phase_diagram(
         BASALT_COMPOSITION.atomic_composition,
-        candidate_phases(),
+        PHASES,
         pressure_range,
         temperature_range,
         settings,
@@ -86,7 +86,7 @@ def refine(source, verbose=False, resolution=None):
     """Resume saved phase lines and optionally refine their point spacing."""
     return refine_saved(
         source,
-        candidate_phases(),
+        PHASES,
         composition=BASALT_COMPOSITION.atomic_composition,
         verbose=verbose,
         resolution=resolution,
@@ -117,6 +117,8 @@ def plot(
         result,
         path,
         label_fontsize,
+        pressure_unit="kbar",
+        temperature_unit="C",
         phase_aliases={"g": "gt"},
         axes=dict(
             xlim=temperature_range,
@@ -130,24 +132,10 @@ def plot(
     )
 
 
-def main():
-    parser = example_parser(
-        __doc__,
-        "basalt_phase_diagram_output",
-        seeds=7,
-        replot=True,
-        refine=True,
-        resolution=False,
-    )
-    return run_phase_diagram_example(
-        parser,
-        lambda args: calculate(args.seeds, args.quick, args.verbose),
-        stem="basalt_phase_diagram",
+if __name__ == "__main__":
+    write_phase_diagram(
+        calculate(seeds=SEEDS, verbose=True),
+        OUTPUT_DIR / "basalt_phase_diagram",
         save_json=save_json,
         plot=plot,
-        refine=refine,
     )
-
-
-if __name__ == "__main__":
-    main()