AZURE2 Documentation

AZURE2 is an R-matrix code for nuclear astrophysics, used to calculate differential and angle-integrated cross sections for resonant nuclear reactions. It provides a graphical user interface for setting up calculations, fitting experimental data, and visualizing results.

The R-matrix portions of the code are based on the formulation of A. M. Lane and R. G. Thomas, Reviews of Modern Physics 30, 257 (1958).

Note

All published works that incorporate results generated by AZURE2 should cite:

R.E. Azuma, E. Uberseder, E.C. Simpson, C.R. Brune, H. Costantini, R.J. deBoer, J. Gorres, M. Heil, P.J. Leblanc, C. Ugalde, and M. Wiescher, Physical Review C 81, 045805 (2010).

Getting Started

• Installation
  • Dependencies
  • Building from Source
  • Docker
• Overview
  • GUI Organization
  • Menus
  • Project Files
  • Workflow Summary
• What AZURE2 Can Do
  • The model
  • Observables
  • Experimental effects
  • Fitting
  • Bayesian inference
  • Scripting
  • Performance
  • Interfaces
  • What AZURE2 does not do

User Guide

• File Menu
• Configure Menu
  • Formalism
  • Check Files
  • Directories
  • Runtime Options
• Particle Pairs Tab
  • Managing Particle Pairs
  • Particle Pair Types
  • Add Particle Pair Dialog
• Levels and Channels Tab
  • Tab Layout
  • Managing Levels
  • Channels
  • Channel Configuration
  • Gamma-Ray Calculations
• Segments Tab
  • Segments From Data
  • Segments Without Data
• Experimental Effects Tab
  • Overview
  • Managing Experimental Effects
  • Add Experimental Effect Dialog
• Fitting Tab
  • Parameter Tables
  • Controls
• How the Chi-Squared Is Built
  • The data term
  • The normalization penalty
  • The energy-shift penalty
  • Nuisance parameters
  • What chiSquared.out actually reports
  • Consistency with the MCMC
• Calculate Tab
  • Calculation Types
  • Minimizer Selection
  • Parameter and Integral Files
  • Execution Controls
• Plot Tab
  • Selecting Segments
  • Drawing Plots
  • Axis Configuration
  • Interacting with Plots
  • Exporting and Printing
• MCMC Tab
  • The sampler
  • Parameters and priors
  • Sampling settings
  • Monitoring a run
  • Output files
  • Resuming
  • Analysing the chain
  • Sampling from Python instead
• pyazr — the Python Interface
  • Installation
  • First steps
  • Two parameter conventions
  • Inspecting a model
  • Chi-squared and derivatives
  • Editing the model
  • Decomposing a cross section
  • Fetching data from EXFOR and NDS
  • Angular distributions
  • Analyzing power
  • Cleaning up
  • Dimensionless widths
  • The external region, and the caches
  • Examples
  • Running in parallel
  • Data mode and extrapolation mode
  • Frames and units

Theory

• Polarization Observables in R-Matrix Theory
  • Why an analyzing power is worth measuring
  • The spin structure of the scattering amplitude
  • Seyler’s expression for the transition matrix
  • The vector analyzing power
  • Four places where the analyzing power must vanish
  • The sign, and why it cannot be checked internally
  • Analyzing power through a target of finite thickness
  • Scope
• Computing the Analyzing Power in AZURE2
  • What the code already had, and the one thing it did not
  • The step that made the rest easy
  • The amplitude matrix
  • Validating it, in the order the checks were applied
  • Making it an observable
  • Averaging a ratio over a target
  • Getting data to test against
  • Fitting it
  • Differentiating it
  • Using it
  • What is not done

Reference

• Data Formats
  • Input Data Files
  • Project Files (.azr)
• Output Files
  • Parameter Files
  • Cross Section Output
  • Uncertainty and Statistics
  • Other Files
• Command-Line Usage
  • Launching the GUI
  • Command-Line Mode
  • Available Options
  • Examples
• Troubleshooting
  • Common Issues
  • Getting Help

Developer Guide

• Developer Guide
  • Level Matrix Construction and Inversion
  • EData, Data Points, and Target Effects
  • Code Architecture
  • Physics Core
  • GUI Structure
  • API Reference
  • Contributing