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PyRITE

  • User Guides
  • Physical Models
  • Computation and Statistics
  • Physics Validation
  • Writeups
    • Development Reference
    • Architecture Decision Records
    • Supported Python API
    • References
  • User Guides
  • Physical Models
  • Computation and Statistics
  • Physics Validation
  • Writeups
  • Development Reference
  • Architecture Decision Records
  • Supported Python API
  • References

Documentation

  • User Guides
    • Getting started
    • Project README
    • pyrite CLI reference
    • pyrite deprecations
    • Python API workflow
    • Persistent shell completion
    • Configuration cookbook
    • Working with results
    • Analysis tutorial
    • Running on a cluster (SLURM)
    • Sweep fidelity and dataset identity
    • External catalogs and workspace data
    • Adding materials
    • Import a GPT electron beam
    • Troubleshooting
  • Physical Models
    • Atomic form factors
    • Elemental transport data
    • Beam phase space
    • Longitudinal bunch structure
    • Electron transport
    • Elastic scattering
    • Atomic-electron angular deflection
    • Stopping power and the energy cutoff
    • Inelastic scattering and energy-loss straggling
    • Shell soft/hard inelastic transport
    • Positron transport
    • Coherent PXR and CBS radiation
    • Coherent-emission tracking
    • Temporal intensity profile
    • Bremsstrahlung
    • Hard BremsLib photon events
    • Characteristic radiation
    • Photon escape and in-medium dispersion
    • Spectral observables and conventions
    • Sample-tilt convention
    • Transport geometry and boundaries
    • Detector solid-angle integration
    • Detector and instrument response
    • Crystal structure representation
    • Structure factor and Debye–Waller
    • Reflection selection
    • Material composition
    • Crystal mosaicity
    • Multilayer film-on-substrate materials
  • Computation and Statistics
    • Execution and acceleration
    • Memory, chunking, and scheduling
    • Precision and tolerances
    • Energy-grid semantics
    • Statistical methods
    • Random number streams
  • Physics Validation
    • Physics validation ledger
      • Core coherent physics (highest risk — verify first)
      • Crystallography & atomic data
      • Crystal structure & CIF provenance
      • Transport & background
      • Mosaicity & multilayer (code-cross-checked; need sign-off + measured data)
      • Detector forward models (downstream — lower risk)
      • Grazing-incidence grating spectrometer
      • Channeling
    • Validation status summary
    • Validation domain inventories
    • Physics validation system
    • atomic-form-factor
    • structure-factor
    • Structural CIF adapter
    • adaptive-sample-size-stopping
    • beam-energy-spread-injection — independent re-derivation
    • Courant–Snyder transverse beam injection
    • Sampled beam phase-space metrics
    • Linear bunch-front tilt
    • GPT GDF electron injection
    • coherent-line-grid-fringe-spacing
    • coherent-line-grid-windowed-resolution
    • Coherent flat-term omission
    • Transverse flat-term omission certificate
    • Bulk dielectric loss candidate
    • EEDL material shell rates
    • elsepa-elastic-sampling
    • ELSEPA positron elastic sampling
    • Bhabha close collisions for positrons
    • SBETHE positron collision stopping
    • Positron bremsstrahlung scaling \(F_p(Z,E)\)
    • In-flight two-photon positron annihilation (Heitler)
    • Positron annihilation at rest
    • elsepa-muffin-tin-inputs
    • inelastic-angular-deflection
    • PENELOPE shell oscillators
    • PENELOPE shell oscillators: independent verification
    • PENELOPE shell GOS moments
    • PENELOPE shell GOS moments: independent verification
    • PENELOPE inner-shell rate substitution and stopping closure
    • Verification: penelope-shell-rate-closure
    • PENELOPE shell GOS soft/hard partition
    • PENELOPE shell hard-loss sampling: independent verification
    • PENELOPE shell hard-event primary recoil
    • PENELOPE shell secondary emission direction
    • Shell soft/hard inelastic transport
    • Shell soft/hard secondary electron transport
    • SBETHE atomic shell inputs
    • SBETHE atomic shell inputs: independent verification
    • SBETHE Si core-edge GOS diagnostic
    • Electron transport — independent re-derivation
    • energy-controlled-propagation
    • energy-loss-straggling
    • energy-step-convergence
    • GOS distant response
    • GOS hard-collision recoil
    • GOS close Møller branch
    • SBETHE optical oscillator quadrature
    • GOS soft/hard transfer partition
    • line-grid-sinc-convergence
    • line-grid-resonance-bandwidth
    • line-grid-resonance-local-spacing
    • Line-spectrum error budget
    • line-window-seeding
    • Historical Joy–Luo/Berger–Seltzer stopping comparison
    • Longitudinal bunch sampling
    • Longitudinal target-line timing
    • radiation-error-estimators
    • Relativistic (Berger–Seltzer) collision stopping — independent re-derivation
    • SBETHE corrected collision stopping in transport
    • SBETHE material inputs
    • substep-radiation-invariance
    • transport-midpoint-stopping
    • cr-debye-b-of-t — site Debye–Waller \(B(T)\) re-derivation
    • cr-mott-bethe-factor — Mott–Bethe numerator in the planar potential
    • cr-planar-continuum-potential — plane-averaged electron potential energy
    • cr-transverse-eigenproblem re-derivation
    • cr-dipole-matrix-element re-derivation
    • cr-initial-occupation re-derivation
    • cr-doppler-line-energy re-derivation
    • cr-mean-inner-potential re-derivation
    • cr-plane-incidence re-derivation
    • cr-lindblad-jump-operators — Lindblad scattering kernels for planar channeling
    • cr-density-matrix-split-operator — paraxial Lindblad solver for planar channeling
    • cr-density-matrix-split-operator: abTEM frozen-phonon oracle
    • cr-mcwf-unravelling — quantum-jump unravelling of the channeling Lindblad equation
    • cr-dechanneling-collapse: Kephart occupation lengths and cutoff sensitivity
    • cr-dipole-rate re-derivation
    • cr-boosted-dipole-angular re-derivation
    • cr-line-shape re-derivation
    • cr-yield-assembly re-derivation
    • cr-capture-bound re-derivation
    • cr-capture-yield re-derivation
    • cr-transition-radiation-bound re-derivation
    • cr-zone-handoff-accounting: the channeling-zone handoff into native transport
    • cr-persisted-channel: the persisted ensemble source
    • quantum-decoherence-budget — cell-averaged transverse decoherence rate re-derivation
    • channeling-modulated-incoherent-emission: independent re-derivation
    • absorption-length
    • brem-source-comparison
    • brem-spectrum
    • bremslib-angular-model
    • bremslib-coupled-expected-spectrum
    • bremslib-radiative-event-spectrum
    • bremslib-radiative-partition
    • cbs-amplitude
    • characteristic-radiation
    • eedl-shell-ionization-comparison
    • bremslib-angular-schiff
    • closed-form-flux
    • coherent-emission
    • Pair-production energy and angle sampling
    • First interaction and pair conversion of coupled hard photons
    • coherent-formation-absorption
    • coherent-inter-electron-decoherence
    • quantum-pair-population-normalization
    • coherent-physical-bunch-population
    • coherent-line-spectrum
    • coherent-segment-midpoint-time
    • temporal-intensity-profile
    • cross-reflection-coherence
    • external-brem-subtraction
    • Finite-footprint longitudinal decoherence
    • finite-time-lineshape
    • Line absorption tabulation
    • Kinematic validity envelope
    • line-energy-dispersion
    • narrow-beam-total-attenuation
    • pxr-amplitude
    • self-absorption
    • segment-escape-average
    • sinc-bin-far-envelope
    • sinc-bin-integration
    • Near/far reduction of the bin-mean line spectrum
    • transverse-bunch-form-factor
    • xray-chi-zero
    • xray-in-medium-propagation-phase
    • xray-in-medium-resonance
    • xray-refractive-index
    • Zhai h-BN 921 nm detected spectrum
    • 2h-tas2-debye-waller-002
    • 2H-a niobium dichalcogenide structures
    • Crystal database external cross-check
    • Debye-Waller provenance and anisotropy validation audit
    • hbn-structure
    • hfs2-structure
    • hopg-debye-waller-00l
    • mos2-debye-waller-00l
    • mosaic-analytic
    • mosaic-mc
    • Multilayer stack transport — independent re-derivation
    • Oriented V2O5 and 1T-TiS2 structures
    • pdte2-debye-waller-001
    • Independent validation: surface-hkl-orientation
    • blazed-groove-geometry
    • finite-beam-size
    • Independent validation: finite transverse crystal
    • Grazing-beam projection — independent re-derivation
    • surface-hkl-orientation
    • alexs-charge-diffusion — independent verification
    • alexs-qe-absorption — independent verification
    • Centred spherical detector acceptance
    • Centred rectangular sensor acceptance
    • detector-eaglexo
    • detector-line-broadening
    • Timepix source-cell bookkeeping
    • grazing-optical-constants, grazing-reflectivity
    • pixel-angular-interpolation
    • Positioned-filter attenuation verification packet
    • External bremsstrahlung comparison and subtraction
    • Validation status: Zhai supplementary coherent-emission studies
  • Writeups
    • Electron Transport Physics Recommendations
    • Recommendation: energy grids across six decades
    • Recommendation: phase-space sampling and variance reduction
    • Relativistic 1–10 MeV electron transport and quantum channeling
    • Relativistic PXR/CBS and polarization: implementation assessment
    • Superradiant PXR: requirements beyond coherent tracking
    • Quantum-coherent CXR emission from shaped and entangled transverse states
    • Mechanisms for phase retention
    • Channeling radiation: physics implementation walkthrough
    • Recommendation: transition radiation through 100 MeV
    • Grazing-incidence soft X-ray grating spectrometer
    • Target and filter object semantics
    • Proposal: parameter-space result prioritization
  • Development Reference
    • Development environment and focused verification
    • Documentation authoring and maintenance
    • Releasing and versioning
    • Rederivation LaTeX/MyST style rules
    • Configuration and profile resolution
    • Materials catalog schema
    • Profile settings reference
    • Data distribution and repository size
    • Core architecture RFC: scene objects, scorers, and API surface
    • Repository map
    • Performance-profile analysis playbook
    • Streaming coherent line RawKernel stage
    • Compute performance optimization history
    • CPU startup latency
    • Phase retention decisions
    • Phase retention: paired GPU measurements
    • GPU electron transport RawKernel
    • JIT spectrum-kernel walkthrough
    • Straggled transport integration
    • Transport JIT-kernel walkthrough
    • In-tree transport preparation adapters
    • Batch emission adapters in existing components
    • Select and extend in-tree physics
    • Physics adapter dispatch overhead
    • Cross-profile checkpoint case store
    • Dataset identity, outputs, and storage
    • Result persistence schema
    • Trajectory artifact storage
    • Trajectory scenes and viewer evaluation
    • Transport outputs
  • Architecture Decision Records
    • 0001 — Adopt architecture decision records
    • 0002 — CLI surface redesign (noun→verb)
    • 0003 — Content-addressed artifact model
    • 0004 — Package & repository structure
    • 0005 — Energy-grid schema decisions
    • 0006 — Consolidate agent work records
    • 0007 — PyRITE project identity and compatibility
    • 0008 — No arbitrary target geometry
    • 0009 — Result persistence format
    • 0010 — Reduce the CLI noun surface
    • 0012 — Track backlog in GitHub Issues, not TODO.md
    • 0013 — Automatic line grids by default
    • 0014 — Packaged data layout
    • 0015 — xraydb as the atomic scattering data source
    • 0016 — Share descriptions across target and filter roles
    • 0017 — Extend physics through in-tree preparation and batch scoring contracts
    • 0018 — Model electron channeling as a quantum entrance zone
  • Supported Python API
    • pyrite.photon_energies
    • pyrite.Beam
    • pyrite.TransverseSpot
    • pyrite.BunchFrontTilt
    • pyrite.PointSpot
    • pyrite.PointBunch
    • pyrite.BunchLength
    • pyrite.Offsets
    • pyrite.GdfSource
    • pyrite.Slab
    • pyrite.Stack
    • pyrite.SubstanceRef
    • pyrite.RectangularBody
    • pyrite.Target
    • pyrite.Filter
    • pyrite.Layer
    • pyrite.Footprint
    • pyrite.BlazedGrooves
    • pyrite.CrystalCut
    • pyrite.PlanarPose
    • pyrite.PixelGrid
    • pyrite.FilterPlate
    • pyrite.Acquisition
    • pyrite.NativeAcquisition
    • pyrite.AcquisitionBatch
    • pyrite.IdealPhotonCounter
    • pyrite.PlanarDetector
    • pyrite.PixelScorer
    • pyrite.ResolvedObservation
    • pyrite.PixelMetadata
    • pyrite.PixelRayMap
    • pyrite.SpectralFactors
    • pyrite.SpatialResult
    • pyrite.Scene
    • pyrite.Sweep
    • pyrite.Physics
    • pyrite.CxrReflections
    • pyrite.Numerics
    • pyrite.Precision
    • pyrite.Analysis
    • pyrite.Result
    • pyrite.Provenance
    • pyrite.CxrSpectra
    • pyrite.SpectralDensity
    • pyrite.fetch_tables
    • pyrite.simulate
    • pyrite.materials.MaterialCatalog
    • pyrite.materials.MaterialConfigError
    • pyrite.materials.MaterialIdentity
    • pyrite.materials.CrystalInfo
    • pyrite.materials.CrystalSpec
    • pyrite.materials.MediumSpec
    • pyrite.materials.MaterialSpec
    • pyrite.materials.MaterialValidationSpec
    • pyrite.materials.ScanSpec
    • pyrite.materials.LayerSpec
    • pyrite.materials.load_material_catalog
    • pyrite.materials.atomic.cromer_mann_f0
    • pyrite.materials.atomic.henke_dispersion
    • pyrite.materials.atomic.atomic_form_factor
    • pyrite.materials.crystal.reciprocal_g_vector
    • pyrite.materials.crystal.structure_factor
    • pyrite.materials.crystal.chi_g
    • pyrite.materials.crystal.U_g
    • pyrite.materials.crystal.absorption_length_ang
    • pyrite.materials.crystal.dominant_reflections
    • pyrite.materials.attenuation.linear_attenuation_inv_mm
    • pyrite.montecarlo.Case
    • pyrite.montecarlo.transport.simulate_trajectories
    • pyrite.montecarlo.spectrum.mc_cxr_spectrum
    • pyrite.montecarlo.spectrum.mc_cxr_spectrum_solid_angle
    • pyrite.montecarlo.spectrum.mc_brem_spectrum
    • pyrite.detectors.response.detector_efficiency
    • pyrite.detectors.response.convolve_detector
    • pyrite.montecarlo.runner.run_case
    • pyrite.montecarlo.runner.run_cases
    • pyrite.detectors.Detector
    • pyrite.AngularAcceptance
    • pyrite.SensorAcceptance
    • pyrite.detectors.EnergyBins
    • pyrite.detectors.NativeSpectrum
    • pyrite.detectors.Timepix3
    • pyrite.detectors.EagleXO
    • pyrite.detectors.LegacyEDS
    • pyrite.detectors.eaglexo_response.EagleResponse
    • pyrite.detectors.eaglexo_response.get_response
    • pyrite.detectors.timepix_response.TimepixResponse
    • pyrite.detectors.timepix_response.get_response
    • pyrite.detectors.grating.Grating
    • pyrite.detectors.grating.SimpleCCD
    • pyrite.detectors.grating.disperse_spectrum
    • pyrite.detectors.grating.detected_image
    • pyrite.results.Settings
    • pyrite.results.records
    • pyrite.results.filter_results
    • pyrite.results.select_results
    • pyrite.results.best_azimuth
    • pyrite.results.cxr_metrics
    • pyrite.results.summary_table
  • References
    • Atomic data sources
  • User Guides

User Guides#

Task-oriented instructions for running and analyzing PyRITE.

New users should begin with Getting started, then use Working with results to understand checkpoint and analysis workflows.

  • Getting started
  • Project README
  • pyrite CLI reference
  • pyrite deprecations
  • Python API workflow
  • Persistent shell completion
  • Configuration cookbook
  • Working with results
  • Analysis tutorial
  • Running on a cluster (SLURM)
  • Sweep fidelity and dataset identity
  • External catalogs and workspace data
  • Adding materials
  • Import a GPT electron beam
  • Troubleshooting

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