burnman-cpp 0.6.0__tar.gz → 0.8.0__tar.gz

{burnman_cpp-0.6.0 → burnman_cpp-0.8.0}/.github/workflows/benchmarks.yml

@@ -43,7 +43,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ catch2 libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Configure benchmarks
         run: |

{burnman_cpp-0.6.0 → burnman_cpp-0.8.0}/.github/workflows/tests.yml

@@ -20,7 +20,7 @@ jobs:
   cpp:
     name: C++ tests
     runs-on: ubuntu-24.04
-    timeout-minutes: 20
+    timeout-minutes: 60
     steps:
       - name: Check out repository
         uses: actions/checkout@v7
@@ -32,7 +32,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ catch2 libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Configure C++ tests
         run: |
@@ -51,7 +51,7 @@ jobs:
   python:
     name: Python ${{ matrix.python-version }} tests
     runs-on: ubuntu-24.04
-    timeout-minutes: 20
+    timeout-minutes: 60
     strategy:
       fail-fast: false
       matrix:
@@ -80,7 +80,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Build and install Python package
         run: python -m pip install '.[test,examples]' -Ccmake.define.BURNMAN_WARNINGS_AS_ERRORS=ON
@@ -92,7 +92,7 @@ jobs:
   reference:
     name: Pinned Python BurnMan reference
     runs-on: ubuntu-24.04
-    timeout-minutes: 20
+    timeout-minutes: 60
     env:
       CMAKE_BUILD_PARALLEL_LEVEL: "2"
       MPLBACKEND: Agg
@@ -128,12 +128,12 @@ jobs:
           sudo apt-get update
           sudo apt-get install -y --no-install-recommends \
             cmake g++ clang-format libeigen3-dev libgsl-dev \
-            libcdd-dev libgmp-dev libnlopt-cxx-dev
+            libcdd-dev libgmp-dev libnlopt-cxx-dev libhdf5-dev
 
       - name: Install wrapper and reference dependencies
         run: |
           python -m pip install '.[test,examples]' -Ccmake.define.BURNMAN_WARNINGS_AS_ERRORS=ON
-          python -m pip install -e 'build/python-burnman-reference[dev]'
+          python -m pip install -e 'build/python-burnman-reference[dev]' h5py
 
       - name: Audit stored reference values and mineral catalogue
         env:
@@ -141,6 +141,7 @@ jobs:
         run: |
           python tools/check_reference_data.py
           python tools/export_example_minerals.py --check
+          python tools/export_covariance_data.py --check
           python tools/generate_ps1994_reference.py --reference build/python-burnman-reference
 
       - name: Run complete Python suite with the pinned reference

{burnman_cpp-0.6.0 → burnman_cpp-0.8.0}/.gitignore

@@ -29,3 +29,4 @@ examples/*_output/
 /benchmark-report.xml
 /python_assemblage_benchmarks.csv
 /python_mineral_benchmarks.csv
+benchmarks/*/results/

{burnman_cpp-0.6.0 → burnman_cpp-0.8.0}/CMakeLists.txt

@@ -13,7 +13,7 @@ endif()
 file(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/pyproject.toml" BURNMAN_VERSION_LINE
      REGEX "^version = ")
 string(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+" BURNMAN_VERSION "${BURNMAN_VERSION_LINE}")
-project(burnman_cpp VERSION ${BURNMAN_VERSION} LANGUAGES CXX)
+project(burnman_cpp VERSION ${BURNMAN_VERSION} LANGUAGES C CXX)
 
 option(BURNMAN_BUILD_PYTHON "Build the Python extension" ON)
 option(BURNMAN_BUILD_TESTS "Build the C++ unit tests" OFF)
@@ -39,6 +39,7 @@ set(BURNMAN_WHEEL_DEPENDENCIES "" CACHE PATH "Private prefix for wheel dependenc
 if(BURNMAN_WHEEL_DEPENDENCIES)
   list(PREPEND CMAKE_PREFIX_PATH "${BURNMAN_WHEEL_DEPENDENCIES}")
   set(GSL_ROOT_DIR "${BURNMAN_WHEEL_DEPENDENCIES}")
+  set(HDF5_ROOT "${BURNMAN_WHEEL_DEPENDENCIES}")
 endif()
 if(APPLE)
   list(APPEND CMAKE_PREFIX_PATH /opt/homebrew /usr/local)
@@ -48,6 +49,7 @@ if(Eigen3_VERSION VERSION_LESS 3.4)
   message(FATAL_ERROR "BurnMan requires Eigen >= 3.4 (found ${Eigen3_VERSION})")
 endif()
 find_package(GSL REQUIRED)
+find_package(HDF5 1.10 REQUIRED COMPONENTS C)
 find_path(NLOPT_INCLUDE_DIR NAMES nlopt.hpp REQUIRED)
 find_library(NLOPT_LIBRARY NAMES nlopt REQUIRED)
 find_path(CDD_INCLUDE_DIR NAMES cdd.h PATH_SUFFIXES cddlib cdd REQUIRED)
@@ -62,6 +64,26 @@ target_include_directories(burnman_core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/inclu
 target_link_libraries(burnman_core PUBLIC Eigen3::Eigen GSL::gsl GSL::gslcblas)
 target_include_directories(burnman_core SYSTEM PRIVATE ${CDD_INCLUDE_DIR} ${GMP_INCLUDE_DIR} ${NLOPT_INCLUDE_DIR})
 target_link_libraries(burnman_core PUBLIC ${CDD_GMP_LIBRARY} ${GMP_LIBRARY} ${NLOPT_LIBRARY})
+target_include_directories(burnman_core SYSTEM BEFORE PRIVATE ${HDF5_INCLUDE_DIRS})
+target_link_libraries(burnman_core PUBLIC ${HDF5_LIBRARIES})
+
+# Embed the HDF5 file images for standalone C++ and installed Python use.
+# CMake performs this step without requiring h5py or a Python interpreter.
+function(burnman_covariance_data name dataset)
+  set(input "${CMAKE_CURRENT_SOURCE_DIR}/src/data/input_covariance/${dataset}_cov.h5")
+  set(output "${CMAKE_CURRENT_BINARY_DIR}/generated/${name}_covariance_data.hpp")
+  set(script "${CMAKE_CURRENT_SOURCE_DIR}/cmake/EmbedCovariance.cmake")
+  add_custom_command(OUTPUT "${output}"
+    COMMAND "${CMAKE_COMMAND}" "-DNAME=${name}" "-DINPUT=${input}"
+            "-DOUTPUT=${output}" -P "${script}"
+    DEPENDS "${input}" "${script}"
+    VERBATIM)
+  target_sources(burnman_core PRIVATE "${output}")
+endfunction()
+burnman_covariance_data(HP11 HP_2011_ds62)
+burnman_covariance_data(HGP18 HGP_2018_ds633)
+burnman_covariance_data(HPx_ds636 HPx_ds636)
+target_include_directories(burnman_core PRIVATE "${CMAKE_CURRENT_BINARY_DIR}/generated")
 set_target_properties(burnman_core PROPERTIES POSITION_INDEPENDENT_CODE ON)
 burnman_compiler_warnings(burnman_core)
 
@@ -74,16 +96,26 @@ if(BURNMAN_BUILD_PYTHON)
     python/bindings/eos.cpp
     python/bindings/materials.cpp
     python/bindings/composition.cpp
+    python/bindings/linear_fitting.cpp
+    python/bindings/composition_fitting.cpp
+    python/bindings/thermobarometry.cpp
+    python/bindings/chemistry.cpp
+    python/bindings/equilibrated_composite.cpp
     python/bindings/combined.cpp
     python/bindings/modifiers.cpp
     python/bindings/solutions.cpp
     python/bindings/minerals.cpp
     python/bindings/utils.cpp
     python/bindings/model_sets.cpp
+    python/bindings/seismic.cpp
+    python/bindings/geotherm.cpp
+    python/bindings/layer.cpp
+    python/bindings/planet.cpp
     python/bindings/polytope.cpp
     python/bindings/phase_diagram.cpp
     python/bindings/equilibration.cpp)
   target_link_libraries(_core PRIVATE burnman_core)
+  set_target_properties(_core PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
   target_compile_definitions(_core PRIVATE BURNMAN_VERSION="${PROJECT_VERSION}")
   burnman_compiler_warnings(_core)
   install(TARGETS _core LIBRARY DESTINATION burnman_cpp RUNTIME DESTINATION burnman_cpp)

{burnman_cpp-0.6.0 → burnman_cpp-0.8.0}/Makefile

@@ -1,12 +1,16 @@
-# Copyright (c) 2025 Benedict Heinen
+# ------------------------------------------------------
 #
-# This file is part of burnman_cpp and is licensed under the
-# GNU General Public License v3.0 or later. See the LICENSE file
-# or <https://www.gnu.org/licenses/> for details.
+# SPDX-License-Identifier: GPL-3.0-or-later
 #
-# burnman_cpp is based on BurnMan: <https://geodynamics.github.io/burnman/>
+# SPDX-FileCopyrightText: Copyright (C) 2025-2026 by the BurnMan Team.
 #
-# ------------------- END OF LICENSE SECTION -----------------
+# This file is part of BurnMan.
+#
+# Detailed license information governing the source code
+# and contributions can be found in the LICENSE document.
+#
+# ------------------------------------------------------
+
 # The native sources implement a library; Catch2 supplies main() for tests.
 TARGET_LIBRARY := libburnman.a
 TEST_EXEC := run_tests
@@ -14,6 +18,8 @@ BENCHMARK_EXEC := run_benchmarks
 
 # Compiler
 CXX := g++
+CMAKE ?= cmake
+PKG_CONFIG ?= pkg-config
 
 # Directories
 CWD := $(shell pwd)
@@ -32,11 +38,14 @@ INCLUDE_DIR_TEST := $(TEST_DIR)/include
 # GSL on MacOS installed via brew is in /opt/homebrew/lib
 EXTRA_INCLUDE ?= $(wildcard /opt/homebrew/include /opt/homebrew/include/eigen3 /opt/homebrew/opt/gsl/include /usr/local/include /usr/local/include/eigen3 /usr/include/eigen3)
 EXTRA_LIB ?= $(wildcard /usr/local/lib /opt/homebrew/lib)
-LDFLAGS_COMMON := -lgsl -lgslcblas -lcddgmp -lgmp -lnlopt -lm
+# Override these flags when HDF5 is installed outside pkg-config's search path.
+HDF5_CFLAGS ?= $(shell $(PKG_CONFIG) --cflags hdf5)
+HDF5_LIBS ?= $(shell $(PKG_CONFIG) --libs hdf5)
+LDFLAGS_COMMON := -lgsl -lgslcblas -lcddgmp -lgmp -lnlopt $(HDF5_LIBS) -lm
 LDFLAGS_TEST := -lCatch2Main -lCatch2
 
 # Expand to paths
-INCLUDE_FLAGS_COMMON := -I$(INCLUDE_DIR) $(addprefix -isystem , $(EXTRA_INCLUDE))
+INCLUDE_FLAGS_COMMON := -I$(INCLUDE_DIR) $(HDF5_CFLAGS) $(addprefix -isystem , $(EXTRA_INCLUDE))
 INCLUDE_FLAGS_TEST := -I$(INCLUDE_DIR_TEST)
 LIB_PATHS := $(addprefix -L, $(EXTRA_LIB))
 
@@ -94,6 +103,12 @@ ifeq ($(PROFILE), 1)
 	MODE_BUILD_DIR := $(MODE_BUILD_DIR)-profile
 endif
 
+# Covariance images are generated for this build mode before their reader.
+COVARIANCE_BUILD_DIR := $(MODE_BUILD_DIR)/generated
+COVARIANCE_EMBED_SCRIPT := $(CWD)/cmake/EmbedCovariance.cmake
+COVARIANCE_HEADERS := $(addprefix $(COVARIANCE_BUILD_DIR)/,HP11_covariance_data.hpp HGP18_covariance_data.hpp HPx_ds636_covariance_data.hpp)
+CPPFLAGS += -I$(COVARIANCE_BUILD_DIR)
+
 # Find source files
 SOURCES := $(shell find $(SRC_DIR) -name '*.cpp')
 TEST_SOURCES := $(shell find $(TEST_DIR) -name '*.cpp')
@@ -115,6 +130,15 @@ BENCHMARK_TARGET := $(BIN_DIR)/$(BENCHMARK_EXEC)$(BIN_SUFFIX)
 # Default rule
 all: $(TARGET)
 
+$(COVARIANCE_BUILD_DIR)/HP11_covariance_data.hpp: $(SRC_DIR)/data/input_covariance/HP_2011_ds62_cov.h5
+$(COVARIANCE_BUILD_DIR)/HGP18_covariance_data.hpp: $(SRC_DIR)/data/input_covariance/HGP_2018_ds633_cov.h5
+$(COVARIANCE_BUILD_DIR)/HPx_ds636_covariance_data.hpp: $(SRC_DIR)/data/input_covariance/HPx_ds636_cov.h5
+
+$(COVARIANCE_HEADERS): $(COVARIANCE_EMBED_SCRIPT)
+	$(CMAKE) "-DNAME=$(patsubst %_covariance_data.hpp,%,$(notdir $@))" "-DINPUT=$(filter %.h5,$^)" "-DOUTPUT=$@" -P "$(COVARIANCE_EMBED_SCRIPT)"
+
+$(MODE_BUILD_DIR)/src/data/covariance.o: $(COVARIANCE_HEADERS)
+
 # Archive the native library; linking an executable would require main().
 $(TARGET) : $(OBJECTS) | $(BIN_DIR)
 	$(AR) rcs $@ $^

{burnman_cpp-0.6.0 → burnman_cpp-0.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: burnman_cpp
-Version: 0.6.0
+Version: 0.8.0
 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
@@ -22,6 +22,7 @@ Provides-Extra: examples
 Requires-Dist: matplotlib>=3.6; extra == "examples"
 Provides-Extra: reference
 Requires-Dist: burnman>=2.1; extra == "reference"
+Requires-Dist: h5py>=3.8; extra == "reference"
 Description-Content-Type: text/markdown
 
 # burnman_cpp

{burnman_cpp-0.6.0 → burnman_cpp-0.8.0}/benchmarks/README.md

@@ -3,6 +3,8 @@ Performance benchmarks
 
 Scientific reference comparisons are kept alongside the timing benchmarks:
 
+- [de Koker, Karki & Stixrude (2013), nine liquid compositions](dekoker_2013/README.md):
+  direct native EOS comparisons with supplement Figures S2–S10 and Table 1.
 - [Stixrude & Lithgow-Bertelloni (2024), Figure 13](stixrude_2024_figure13/README.md):
   pyrolite phase modes, native iron and ferropericlase spin along a 1600 K
   surface isentrope, with overlays on the published panels and saved equilibria.
@@ -10,6 +12,9 @@ Scientific reference comparisons are kept alongside the timing benchmarks:
   three lower-mantle shear-velocity profiles, relaxed pyrolite expansivity and
   phase boundaries, with a 1400 K isentrope plus a basal erfc thermal layer.
 
+The illustrative [de Koker mixing and melting reconstruction](../examples/example_dekoker_2013.py)
+is an example, separate from the nine-composition EOS benchmark.
+
 `core/` and `eos/` contain the Catch2 performance benchmarks. They build into
 their own executable and reuse the fixtures in `tests/include/`. Unit tests
 build separately. The Python scripts time pure Python BurnMan, process native

burnman_cpp-0.8.0/benchmarks/dekoker_2013/README.md

@@ -0,0 +1,43 @@
+# Nine DKS liquid-composition comparisons
+
+Compare the unmodified native `dks_l` models for **MgO, Mg5SiO7, Mg2SiO4,
+Mg3Si2O7, MgSiO3, MgSi2O5, MgSi3O7, MgSi5O11 and SiO2** with de Koker,
+Karki & Stixrude (2013).
+
+```sh
+python benchmarks/dekoker_2013/benchmark.py
+```
+
+The benchmark contains only individual-composition EOS comparisons:
+
+- Nine P–V/E–V overlays on the original supplement Figures S2–S10.
+- Six Table 1 properties for each composition at 0 GPa, 3000 K: molar volume,
+  bulk modulus, entropy, Cv, Cp and Grüneisen parameter.
+
+Outputs are saved in `results/`: `endmember_comparisons.pdf` contains all nine
+comparisons, with separate `<composition>_comparison.pdf/png` files, Table 1
+CSV/JSON and sampled isotherms. Units are per mole of the named formula;
+Cv and Cp are normalized by the number of atoms times R. Energy curves omit
+volumes where the native stable volume solve does not return the same branch.
+The overlays are visual comparisons; the Table 1 report records quantitative
+differences and the paper's printed uncertainties.
+
+The catalogue bulk moduli of MgO and Mg5SiO7 exceed Table 1 by 0.0661 and
+0.0336 GPa (1.32 and 1.68 printed uncertainties). The other checked properties
+lie within their printed uncertainties. These differences are reported;
+the benchmark does not adjust catalogue parameters to remove them.
+
+NumPy and Matplotlib are required. Original panels and vector-tick registrations
+are saved in `reference/`, so the benchmark runs without Python BurnMan, the
+original PDF, or Poppler. To regenerate that independent source material,
+place the supplied PDF at `~/deKoker_2013.pdf` and run:
+
+```sh
+python benchmarks/dekoker_2013/extract_reference.py
+```
+
+There is no continuous mixing fit, entropy recalibration or phase diagram in
+this benchmark. Those calculations are the separate
+[MgO–SiO₂ example](../../examples/example_dekoker_2013.py).
+
+Source: [doi:10.1016/j.epsl.2012.11.026](https://doi.org/10.1016/j.epsl.2012.11.026).

burnman_cpp-0.8.0/benchmarks/dekoker_2013/benchmark.py

@@ -0,0 +1,235 @@
+# SPDX-License-Identifier: GPL-3.0-or-later
+# SPDX-FileCopyrightText: Copyright (C) 2025-2026 by the BurnMan Team.
+"""Compare the nine native DKS liquid EOSs with the original paper.
+
+Only individual-composition P(V,T), E(V,T) and Table 1 properties are compared.
+No mixing projection, entropy reset, solid model or melting calculation.
+Run: python benchmarks/dekoker_2013/benchmark.py
+Settings and main(); no command-line arguments.
+"""
+
+import csv
+import json
+from pathlib import Path
+
+import matplotlib.image as mpimg
+import matplotlib.pyplot as plt
+from matplotlib.backends.backend_pdf import PdfPages
+from matplotlib.lines import Line2D
+import numpy as np
+
+import burnman_cpp as bm
+
+REFERENCE_DIR = Path(__file__).with_name("reference")
+OUTPUT_DIR = Path(__file__).with_name("results")
+SHOW_PLOTS = False
+VOLUME_SAMPLES = 401
+
+
+def load_reference():
+    return json.loads((REFERENCE_DIR / "endmembers.json").read_text())
+
+
+def native_table_1(phase):
+    phase.set_state(0.0, 3000.0)
+    nR = sum(phase.formula.values()) * bm.constants.gas_constant
+    return dict(
+        volume_cm3_mol=phase.molar_volume * 1.0e6,
+        K_T_GPa=phase.isothermal_bulk_modulus_reuss * 1.0e-9,
+        entropy_J_mol_K=phase.molar_entropy,
+        Cv_per_nR=phase.molar_heat_capacity_v / nR,
+        Cp_per_nR=phase.molar_heat_capacity_p / nR,
+        grueneisen=phase.grueneisen_parameter,
+    )
+
+
+def axis_value(coordinate, ticks):
+    (v0, c0), (v1, c1) = ticks
+    return v0 + (coordinate - c0) * (v1 - v0) / (c1 - c0)
+
+
+def internal_energy_at_volumes(phase, temperature, volumes, pressures):
+    """Read native energies only where V(P(V,T),T) returns the same branch."""
+    energies = np.full(len(volumes), np.nan)
+    for i, (volume, pressure) in enumerate(zip(volumes, pressures)):
+        try:
+            phase.set_state(pressure, temperature)
+            if np.isclose(phase.molar_volume, volume, rtol=1e-10, atol=1e-16):
+                energies[i] = phase.molar_internal_energy / 1e3
+        except (ValueError, RuntimeError):
+            continue
+    return energies
+
+
+def comparison_figure(phase, reference):
+    x0, y0, x1, y1 = reference["crop"]
+    width = 10.0
+    image_height = width * (y1 - y0) / (x1 - x0)
+    fig = plt.figure(figsize=(width, image_height + 0.9))
+    fraction = image_height / fig.get_figheight()
+    bg = fig.add_axes([0, 0, 1, fraction])
+    bg.imshow(
+        mpimg.imread(REFERENCE_DIR / f"{reference['composition']}.png"), alpha=0.5
+    )
+    bg.set_axis_off()
+    fig.text(
+        0.5,
+        0.98,
+        f"{reference['composition']} liquid: native DKS EOS / Figure {reference['supplement_figure']}",
+        ha="center",
+        va="top",
+        fontsize=13,
+    )
+    handles = [
+        Line2D([], [], color=".6", label="Original LFTR fits and FPMD points (faint)")
+    ]
+    temperatures = reference["temperatures_K"]
+    colors = plt.get_cmap("plasma")(np.linspace(0.05, 0.9, len(temperatures)))
+    handles += [
+        Line2D([], [], color=c, ls="--", label=f"{t:g} K")
+        for t, c in zip(temperatures, colors)
+    ]
+    fig.legend(
+        handles=handles,
+        loc="upper center",
+        bbox_to_anchor=(0.5, 1 - 0.32 / fig.get_figheight()),
+        ncol=4,
+        frameon=False,
+        fontsize=8,
+    )
+    eos = bm.make_eos("dks_l")
+    params = phase.params
+    rows = []
+    for quantity, spec in reference["panels"].items():
+        left, top, right, bottom = spec["bounds"]
+        ax = fig.add_axes(
+            [
+                (left - x0) / (x1 - x0),
+                (y1 - bottom) / (y1 - y0) * fraction,
+                (right - left) / (x1 - x0),
+                (bottom - top) / (y1 - y0) * fraction,
+            ],
+            frameon=False,
+        )
+        ax.set(
+            xlim=[axis_value(x, spec["volume_ticks_cm3_mol"]) for x in (left, right)],
+            ylim=[axis_value(y, spec["quantity_ticks"]) for y in (bottom, top)],
+        )
+        ax.set_axis_off()
+        volumes = np.linspace(*ax.get_xlim(), VOLUME_SAMPLES) * 1.0e-6
+        for temperature, color in zip(temperatures, colors):
+            pressures = [
+                eos.compute_pressure(temperature, float(v), params) for v in volumes
+            ]
+            values = (
+                np.array(pressures) / 1.0e9
+                if quantity == "P"
+                else internal_energy_at_volumes(phase, temperature, volumes, pressures)
+            )
+            if np.count_nonzero(np.isfinite(values)) < 3:
+                raise RuntimeError(
+                    f"No stable {quantity} curve for {phase.name} at {temperature} K"
+                )
+            ax.plot(volumes * 1e6, values, color=color, ls="--", lw=1.1)
+            rows.extend(
+                [
+                    reference["composition"],
+                    temperature,
+                    quantity,
+                    float(v),
+                    float(value),
+                ]
+                for v, value in zip(volumes, values)
+                if np.isfinite(value)
+            )
+    return fig, rows
+
+
+def main():
+    OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
+    reference = load_reference()
+    results, isotherms, table_rows = [], [], []
+    with PdfPages(OUTPUT_DIR / "endmember_comparisons.pdf") as pdf:
+        for row in reference["compositions"]:
+            name = row["composition"]
+            phase = getattr(bm.minerals.DKS_2013_liquids, name + "_liquid")()
+            calculated = native_table_1(phase)
+            comparison = {}
+            for prop, native in calculated.items():
+                source = row["table_1"][prop]
+                delta = native - source["value"]
+                comparison[prop] = dict(
+                    **source,
+                    native=native,
+                    native_minus_paper=delta,
+                    difference_in_printed_uncertainties=delta
+                    / source["printed_uncertainty"],
+                )
+                table_rows.append(
+                    [
+                        name,
+                        prop,
+                        source["value"],
+                        native,
+                        delta,
+                        source["printed_uncertainty"],
+                    ]
+                )
+            results.append(dict(composition=name, properties=comparison))
+            fig, rows = comparison_figure(phase, row)
+            pdf.savefig(fig)
+            for extension in ("pdf", "png"):
+                fig.savefig(OUTPUT_DIR / f"{name}_comparison.{extension}", dpi=200)
+            isotherms.extend(rows)
+            if not SHOW_PLOTS:
+                plt.close(fig)
+            print(
+                f"Compared {name}: Figure {row['supplement_figure']} and Table 1",
+                flush=True,
+            )
+    for filename, fields, rows in (
+        (
+            "table_1_comparison.csv",
+            [
+                "composition",
+                "property",
+                "paper",
+                "native",
+                "native_minus_paper",
+                "printed_uncertainty",
+            ],
+            table_rows,
+        ),
+        (
+            "isotherms.csv",
+            [
+                "composition",
+                "temperature_K",
+                "quantity",
+                "volume_m3_mol",
+                "value_GPa_or_kJ_mol",
+            ],
+            isotherms,
+        ),
+    ):
+        with (OUTPUT_DIR / filename).open("w", newline="") as stream:
+            writer = csv.writer(stream)
+            writer.writerow(fields)
+            writer.writerows(rows)
+    report = dict(
+        source=reference["source"],
+        source_pdf_sha256=reference["source_pdf_sha256"],
+        burnman_cpp_version=bm.__version__,
+        scope="Nine independent liquid compositions only; no continuous mixing or phase diagram",
+        comparisons=results,
+    )
+    (OUTPUT_DIR / "endmember_comparisons.json").write_text(
+        json.dumps(report, indent=2) + "\n"
+    )
+    if SHOW_PLOTS:
+        plt.show()
+    plt.close("all")
+
+
+if __name__ == "__main__":
+    main()