PhaseSmith

PhaseSmith is an early-stage powder-diffraction computation library with a Rust numerical core and a typed Python/NumPy API. The current implementation includes symmetric TCH, CW U/V/W/X/Y broadening, FCJ asymmetry, wavelength components, extensible sample physics, multi-phase CW X-ray/neutron and neutron TOF calculation, plus a first-class scripted Le Bail workflow. Analytical derivatives are computed during fused peak accumulation. The crystallography foundation includes native general-cell mathematics, P1 complex structure factors, exact symmetry, bounded reflection generation, and prepared X-ray and neutron scattering factors with analytical derivatives. General-symmetry structural intensities and monochromatic structural patterns now have a fused native values/JVP/VJP path, direct fixed CIF anisotropic displacement, and a scriptable RietveldPhase API. CIF-backed Le Bail can refine setting-aware lattice parameters with analytical derivatives and guarded, stable-ID reflection-domain regeneration. The first full CIF-backed Rietveld workflow now refines CW profile/background, phase scale, lattice, symmetry-allowed coordinates, occupancy, and isotropic displacement through matrix-free Rust JVP/VJP products with safe checkpoints and structured logs. Model-independent preprocessing now includes a native Smooth Bruckner background implementation compatible with pinned xypattern/Dioptas behavior, plus optional Chebyshev compression and plain NumPy subtraction results.

Install the Python interface from PyPI or the native Rust facade from crates.io:

python -m pip install phasesmith
cargo add phasesmith

Use the versioned documentation to follow the shortest path from powder data and a CIF to background subtraction, Le Bail extraction, Rietveld refinement, reports, and persistence. Documentation sources live in docs, and the architecture and non-negotiable numerical rules are in PROJECT_BRIEF.md. The tag-driven GitHub/PyPI/crates.io process is documented in docs/releasing.md.

Development

Requires Rust 1.85 or newer, Python 3.11 or newer, uv, and maturin.

uv venv
uv pip install -e '.[dev]'
maturin develop --uv
cargo test --workspace --all-features
uv run pytest

Editable environments retain the absolute checkout location. After moving or renaming the repository, recreate .venv, repeat the three setup commands above, and confirm uv run python -c "import phasesmith; print(phasesmith.__file__)" points into the current checkout before running the gate.

Native GUI applications

GUI applications are separate consumers of the published Rust library. A future Tauri or other native application can depend on phasesmith, own its presentation state and background jobs, and call the native workflows directly without bundling Python.

Run the Rust benchmarks with cargo bench -p phasesmith-core. For a comparable optimized Python-to-Rust measurement, build the release extension and require release mode explicitly:

maturin develop --release --uv
uv run python benchmarks/profile.py --require-release
uv run python benchmarks/lebail.py --require-release
uv run python benchmarks/scattering.py --require-release
uv run python benchmarks/structural_pattern.py --require-release
uv run python benchmarks/lattice_refinement.py --require-release
uv run python benchmarks/background.py --require-release
uv run python benchmarks/real_data.py --require-release

The joint multi-histogram PbSO4 workload is also executable entirely in Rust, without building or launching Python:

cargo run --release -p phasesmith-workflows --example joint_pbso4 -- \
  validation/data/gsasii-pbso4-cw

Checksum-pinned validation also has a Python-free CLI. Successful runs write the same stable JSON report used by the scripting adapter:

cargo run -p phasesmith-validation --bin phasesmith-validation -- datasets
cargo run --release -p phasesmith-validation --bin phasesmith-validation -- \
  run iucr-qarr-1g validation/data/iucr-qarr-1g

Ordinary phasesmith.validation calls delegate to these Rust workflows. Python callbacks, custom execution policies, and explicit reference tests keep the independent scripting path; the native CLI does not launch Python.

The real-data benchmark verifies pinned QARR 1g, APS sucrose, and official PbSO4 X-ray/neutron tutorial inputs, records cold and warmed complete-workflow timings, and hashes the timing-free scientific report. By default it compares one- and two-thread QARR execution and runs both PbSO4 probes. Use --dataset, --threads, and --json-output to select cases and retain a machine-readable result. This is the PhaseSmith-only performance harness; the paired QARR and PbSO4 GSAS-II commands below are cross-implementation scientific and performance gates. The corresponding slow regression tests are opt-in:

uv run pytest -m real_data

The pinned external-oracle environment can compare the same support-limited CW profile-and-derivative workload against GSAS-II. A second benchmark starts from the crystal structure and compares structure factors, integrated intensities, and the composed structural CW pattern. Numerical agreement is checked before timings are reported:

uv run python benchmarks/compare_gsasii.py --require-release \
  --gsas-python /path/to/gsas/python \
  --gsas-root /path/to/pinned/GSAS-II \
  --binary-dir /path/to/compatible/GSASII-bin/platform-directory

uv run python benchmarks/compare_gsasii_structural.py --require-release \
  --gsas-python /path/to/gsas/python \
  --gsas-root /path/to/pinned/GSAS-II \
  --binary-dir /path/to/compatible/GSASII-bin/platform-directory

uv run python benchmarks/compare_gsasii_qarr.py --require-release \
  --gsas-python /path/to/gsas/python \
  --gsas-root /path/to/pinned/GSAS-II \
  --binary-dir /path/to/compatible/GSASII-bin/platform-directory \
  --data-directory validation/data/iucr-qarr-1g \
  --phasesmith-threads 2

uv run python benchmarks/compare_gsasii_pbso4.py --require-release \
  --gsas-python /path/to/gsas/python \
  --gsas-root /path/to/pinned/GSAS-II \
  --binary-dir /path/to/compatible/GSASII-bin/platform-directory \
  --data-directory validation/data/gsasii-pbso4-cw

The exact scope and interpretation are documented in docs/gsasii-performance.md. This is a kernel-level comparison. The QARR and PbSO4 drivers separately compare complete native workflows and gate their reported scientific results before reporting speed. The established Python PbSO4 report includes the supplied reference cell alongside the per-probe staged fits and GSAS-II's joint refinement. The Rust example separately exercises PhaseSmith's first-class summed joint objective.

Background estimation is an explicit preprocessing step:

import phasesmith

subtracted = phasesmith.SmoothBrucknerBackground(
    smooth_width=0.1,
    iterations=50,
    chebyshev_order=50,
).subtract(two_theta, measured)

pattern = phasesmith.PowderPattern(
    two_theta,
    observed_y=measured,
    background=subtracted.background,
)

Set chebyshev_order=None to use the raw Bruckner envelope. Neither xypattern nor Dioptas is required at runtime.

Refinement treats that array as a fixed broad baseline. Attach a low-order analytical correction rather than replacing it:

from phasesmith.refinement import ChebyshevBackground, lebail

residual = ChebyshevBackground("residual", (0.0, 0.0, 0.0), (two_theta[0], two_theta[-1]))
request = lebail.LeBailInput(pattern, instrument, phases).with_refinable_background(residual)
result = lebail.refine(request)

Structural Rietveld uses the same additive convention through RietveldInput.background; linear CW Le Bail backgrounds are eliminated by a weighted least-squares update each cycle, while nonlinear background terms remain in the joint analytical solve.

import numpy as np
from phasesmith import accumulate

x = np.linspace(20.0, 30.0, 10_001)
result = accumulate(
    x,
    positions=[24.0, 26.0],
    intensities=[100.0, 80.0],
    fwhms=[0.08, 0.1],
    etas=[0.3, 0.5],
)
print(result.y.shape, result.derivatives.local.values.shape)

# Dense materialization is explicit and intended for small compatibility uses.
dense = result.derivatives.local.to_dense(result.y.size)
print(dense.shape)  # (peak, parameter, sample)

Use profile_tch or accumulate_tch when Gaussian and Lorentzian component FWHMs are the direct inputs. Explicit tch_shape_from_gaussian_sigma and profile_tch_from_gaussian_sigma helpers are provided when Gaussian width is a standard deviation; width conventions are never inferred.

An entire constant-wavelength reflection list, including all local and shared instrument derivatives, is also one array-oriented call:

from phasesmith import ConstantWavelengthInstrument, accumulate_cw

instrument = ConstantWavelengthInstrument(
    wavelength_angstrom=1.54056,
    u_deg2=2e-4,
    v_deg2=-1e-4,
    w_deg2=1.2e-4,
    x_deg=1.5e-3,
    y_deg=3e-3,
)
cw = accumulate_cw(x, [24.0, 26.0], [100.0, 80.0], instrument)
print(cw.derivatives.local_parameter_names)  # intensity, position
print(cw.derivatives.global_parameter_names)  # U, V, W, X, Y

Atomic scattering models are also script-first and can be prepared once for a structure. X-ray species select exact neutral/ionic table states, while neutron species retain natural/isotope identity:

from phasesmith import ScatteringSpecies, XrayNonResonant

species = (
    ScatteringSpecies("Si"),
    ScatteringSpecies("O"),
    ScatteringSpecies("Fe", charge=3),
)
scattering = XrayNonResonant().prepare(species).evaluate([0.0, 0.5, 1.0])
print(scattering.amplitudes.shape)  # (reflection, site)
print(scattering.d_amplitudes_d_s.shape)  # analytical df/ds, same shape

A typed structure can be evaluated without assembling scattering arrays or looping over atoms/reflections in Python. Correction geometry is explicit; the default neutral model returns raw multiplicity-weighted structural intensity:

from phasesmith import XrayNonResonant, calculate_structure_factor_values
from phasesmith.io.cif import read_cif

structure = read_cif("phase.cif").structure
structural = calculate_structure_factor_values(
    structure,
    hkl=[[1, 0, 0], [1, 1, 0]],
    multiplicity=[6, 12],
    scattering=XrayNonResonant(),
    scale=1.0,
)
print(structural.f, structural.integrated_intensity)

Use calculate_structure_factors when the bounded dense analytical structural Jacobian is also required.

Axial divergence is a separate typed model and composes with CW broadening without expanding reflections in Python:

from phasesmith import FcjGeometry, accumulate_cw_fcj

geometry = FcjGeometry(sample_over_radius=0.012, detector_over_radius=0.012)
asymmetric = accumulate_cw_fcj(x, [24.0, 26.0], [100.0, 80.0], instrument, geometry)
print(asymmetric.derivatives.global_parameter_names)
# U, V, W, X, Y, sample_over_radius, detector_over_radius

Discrete radiation components are optional. The ordinary CW calls above are monochromatic; a K-alpha doublet is an explicit model:

from phasesmith import WavelengthComponents, accumulate_cw_fcj_components

radiation = WavelengthComponents.doublet(
    reference_wavelength_angstrom=1.54056,
    secondary_wavelength_angstrom=1.54439,
    secondary_to_reference_intensity=0.5,
)
doublet = accumulate_cw_fcj_components(
    x, [24.0, 26.0], [100.0, 80.0], instrument, radiation, geometry
)

Sample physics is explicit and provider-based. Built-in and third-party models return the same vectorized contribution schema, and Python is never called from the native peak/sample loop:

from phasesmith import (
    CompositePhysicsProvider,
    IsotropicMicrostrainBroadening,
    IsotropicSizeBroadening,
    ReflectionGeometryBatch,
    calculate_cw_pattern,
)

reflections = ReflectionGeometryBatch(
    hkl=[[1, 0, 0], [1, 1, 0]],
    d_spacing_angstrom=[3.72, 2.64],
    two_theta_deg=[24.0, 34.0],
    base_integrated_intensity=[100.0, 80.0],
)
sample = CompositePhysicsProvider(
    (
        IsotropicSizeBroadening(crystallite_size_nm=50.0),
        IsotropicMicrostrainBroadening(rms_microstrain=5e-4),
    )
)
calculated = calculate_cw_pattern(x, reflections, instrument, physics=sample)
print(calculated.derivatives.global_parameter_names)

The high-level script interface assigns durable IDs and calculates all phases through one flattened native call:

from phasesmith import Phase, PowderPattern, ReflectionBatch, calculate_pattern

alpha_reflections = ReflectionBatch(
    reflection_ids=["alpha-100", "alpha-110"],
    hkl=[[1, 0, 0], [1, 1, 0]],
    d_spacing_angstrom=[3.72, 2.64],
    two_theta_deg=[24.0, 34.0],
    integrated_intensity=[100.0, 80.0],
)
alpha = Phase(
    phase_id="alpha",
    name="Alpha phase",
    reflections=alpha_reflections,
    scale=1.0,
    physics=sample,
)
pattern_result = calculate_pattern(PowderPattern(x), instrument, [alpha])
print(pattern_result.reflection_keys)
print(pattern_result.derivatives.global_parameter_names)

Neutron CW is an explicit monochromatic probe configuration and cannot receive an X-ray K-alpha doublet:

from phasesmith import ConstantWavelengthExperiment, calculate_neutron_pattern

neutron = ConstantWavelengthExperiment.neutron(instrument)
neutron_result = calculate_neutron_pattern(PowderPattern(x), neutron, [alpha])

TOF reflections use d-spacing as their durable local coordinate. Values and all local/shared derivatives are accumulated in one native call. Rust and Python consumers can additionally use TofLeBailInput and refine_tof_lebail for a typed microsecond-domain, fixed-instrument nonnegative extraction workflow. Rust callers may attach TofChebyshevBackground to refine an explicit-domain Chebyshev residual on top of the fixed pattern background; omitting it preserves the fixed background alone. Python can build a complete fixed-instrument request from one bank, calibration, and CIF:

from phasesmith.refinement import (
    TofLeBailCancellation,
    TofLeBailInput,
    TofLeBailOptions,
    refine_tof_lebail,
)

request = TofLeBailInput.from_files(
    "PG3_17541.gsa",
    "PGHR_60-2015A.prm",
    "LaB6.cif",
    bank=2,
)
cancellation = TofLeBailCancellation()
events = []
result = refine_tof_lebail(
    request,
    TofLeBailOptions(cycles=20),
    cancellation=cancellation,
    progress=events.append,
)

# Continue a last-accepted state with a larger total cycle budget.
continued = refine_tof_lebail(
    request,
    TofLeBailOptions(cycles=50),
    checkpoint=result.checkpoint,
)

The file path is not tied to POWGEN: reduced center/density columns, GSAS SLOG FXYE, and packed constant-step GSAS STD are supported, and legacy GSAS profile functions 1 and 3 translate into the same typed coefficients. Other beamlines can pass TofPowderPattern and TofInstrument directly. The pinned LANL nickel example is the non-POWGEN acceptance gate for this supported profile family.

The lower-level profile API remains available:

from phasesmith import TofInstrument, accumulate_tof

tof_instrument = TofInstrument(
    zero_us=-0.773,
    difc_us_per_angstrom=5084.83,
    difa_us_per_angstrom2=-2.63,
    difb_us_angstrom=0.0,
    alpha_coefficient=5.0,
    beta0_per_us=0.0333,
    beta1_angstrom4_per_us=0.000964,
    betaq_angstrom2_per_us=0.0,
    sigma0_us2=0.0,
    sigma1_us2_per_angstrom2=15.14,
    sigma2_us2_per_angstrom4=0.0,
    sigmaq_us2_per_angstrom=0.0,
    x_us_per_angstrom=0.0,
    y_us_per_angstrom2=0.0,
    z_us=0.0,
)
tof_x = np.linspace(2_000.0, 20_000.0, 6_001)  # bin centers, microseconds
tof_result = accumulate_tof(tof_x, [0.8, 1.5], [100.0, 80.0], tof_instrument)
print(tof_result.derivatives.local_parameter_names)  # intensity, d_spacing
print(tof_result.derivatives.global_parameter_names)  # 15 instrument rows

A complete Le Bail extraction uses the same typed pattern, instrument, and phase models and requires no project file or hand-written optimizer callback:

from phasesmith.refinement import lebail

observed = PowderPattern(
    x,
    observed_y=measured_y,
    background=background_y,
    uncertainty=sigma_y,
)
result = lebail.refine(lebail.LeBailInput(observed, instrument, (alpha,)))
print(result.termination_reason, result.metrics.rwp)
print([(item.reflection_id, item.integrated_intensity) for item in result.intensities])

For a CIF-backed single phase, the convenience constructor creates the generated reflection domain and the symmetry-allowed bounded lattice parameter set directly from the observed grid:

request = lebail.LeBailInput.from_cif(
    observed,
    instrument,
    "phase.cif",
    phase_id="alpha",
)
result = lebail.refine(request)
print(result.phases[0].structure.cell)

When detector geometry and wavelength are already known from Dioptas/pyFAI but no separate resolution standard was measured, a predominantly single-phase pattern can provide a conservative effective starting profile:

start = starting_profile_from_fwhm(wavelength_angstrom, fwhm_deg=0.04)
request = lebail.LeBailInput.from_cif(
    observed,
    start,
    "dominant-phase.cif",
    phase_id="dominant",
    refine_lattice=True,
)
profile_start = estimate_effective_profile(
    request,
    ProfileEstimationOptions(align_lattice=True),
)
print(profile_start.instrument, profile_start.active_parameters)

The wavelength is fixed. The returned widths may include sample broadening and are intended as refinement starting values, not as an instrument-only resolution calibration. See docs/effective-profile-estimation.md.

A monochromatic structural refinement is likewise constructed directly from a CIF. Parameter families are explicit and no GSAS-II installation is involved:

from phasesmith.refinement import rietveld

request = rietveld.RietveldInput.from_cif(
    observed,
    experiment,
    "phase.cif",
    phase_id="alpha",
    selection=rietveld.RietveldParameterSelection(
        phase_scale=True,
        lattice=True,
        coordinates=False,
        occupancy=False,
        u_iso=False,
    ),
)
result = rietveld.refine(request)
print(result.termination_reason, result.metrics.rwp)
print(result.phases[0].structure.cell)

Multiphase calculations and Rietveld refinement can use a bounded worker pool. The bounded default is two threads. Embedding applications that already schedule independent work can select one thread; choose another fixed budget for predictable GUI/script behavior, or None to use the available logical CPUs:

import phasesmith
from phasesmith.refinement import rietveld

options = rietveld.RietveldOptions(
    execution=phasesmith.ExecutionPolicy(threads=2),
)
result = rietveld.refine(request, options)

Independent phases execute concurrently, while their values and analytical derivatives are combined in the original phase order.

For long-running scripts and application integration, the small project facade keeps restart state, cooperative stop control, persistence, and plain reports together while leaving RietveldInput fully accessible:

from dataclasses import replace

from phasesmith import BraggBrentanoGeometry, RietveldParameterSelection, RietveldProject

experiment = replace(
    experiment,
    zero_shift_deg=0.0,
    geometry=BraggBrentanoGeometry(240.0, sample_displacement_mm=0.0),
)
selection = RietveldParameterSelection(
    phase_scale=True,
    lattice=True,
    sample_physics=True,
    instrument_parameters=("zero_shift_deg", "sample_displacement_mm"),
    background=True,
)
request = replace(request, experiment=experiment, selection=selection)
project = RietveldProject(request)
proposal = project.propose_intelligent_recipe()
print(proposal.to_record())  # advice and rationale; no refinement has run yet
workflow = project.refine_intelligently(logger=my_event_logger)
result = workflow.final_result
project.write_reports(json_path="result.json", csv_path="pattern.csv")
project.save("run-state")

# Another thread or a callback can stop safely; the accepted state is resumable.
project.stop("user_requested")

The intelligent path is optional workflow orchestration. project.refine() continues to call the general solver once with exactly the caller-selected parameters, and project.refine_recipe(recipe) runs an explicit user-defined sequence.

Refinable backgrounds share one analytical interface. Built-ins include power and Chebyshev series, fixed-knot linear interpolation, broad normalized Gaussian amorphous components, and ordered composites. Smooth Bruckner remains an explicit preprocessing operation and is never inserted automatically; when supplied, its values remain the fixed baseline beneath the refinable model.

GSAS-II is used only as the optional pinned validation oracle described in oracle/README.md.

License

PhaseSmith is licensed under the MIT License. GSAS-II is separately licensed, is used only as an optional external validation oracle, and is not redistributed here.