rietx manual

Release 1.0.1. The manual is in two parts.

Part 1 — Using rietx is the task-ordered guide to the package and its public API: install it, run a fit, understand what the fit did, read the report it hands back, and drive it from a program. It assumes you know powder diffraction and not this package.

Part 2 — Theory is the equations behind that machinery, numbered and cross-referenced, with the conventions that decide whether a number transfers between Rietveld codes.

Who this is written for

This manual is written for a person to read.

Parts of the package are not. rietx is built for automated and agentic workflows, and several of its surfaces are shaped for a program to read first: the FitReport and its three layers, agent.refine_json and its JSON envelope, capabilities(), the streaming event ladder, and the diagnostic codes. They are documented here because a person has to understand them to trust, debug or extend what a machine does with them. FitReport also answers a question anyone looking at a plot has: where is this model wrong, and how much of that will the package stand behind?

Notes about that half carry a marker, so you can see at a glance who a paragraph is addressed to:

For agents

This style marks the machine-facing half. Read these notes if you are an agent, or are writing one. Skip them if you are refining a pattern.

If you are an agent reading this manual, read docs/AGENT_PROTOCOL.md first, then come back here for the object model. The protocol says what to do in what order, what to check before believing a number, and which measured findings should change what you do. This manual describes the surface, and nothing here restates the protocol.

How to read this manual

The code is authoritative. Every physics function in rietx cites its reference — author, year, journal — in its docstring, and the long derivations live in the module docstrings. This manual organises that material into numbered equations in Part 2 and into a task order in Part 1. It does not replace it. Where this manual and a docstring disagree, the docstring wins, and the disagreement is a bug worth reporting.

Both parts are guarded against drifting from the code, by different mechanisms, because they fail in different ways. In Part 2 every threshold and fenced constant is injected from the live package when the manual builds, so a renamed constant breaks the build; each displayed equation carries a Source line naming the symbol it was transcribed from, and a test imports every one of them. In Part 1 every dotted name and every parameter dot-path resolves against the live package, every fenced example either runs or states why it cannot, and the walkthroughs are scripts from examples/ included verbatim and executed by the test suite.

Names follow Python’s own convention, so their case tells you what they are. Refinement, RefinementResult and FitReport are capitalised because they are classes. refine, read_pattern and capabilities are functions, rietx.viz.compare is a module, and PLAN_INFO is a module-level constant. A capital does not mean a name matters more.

One consequence changes what you type. A method or a field is written under the class that defines it, not under the variable you would hold it in. RefinementResult.plot means “the plot method of a RefinementResult”, and in your own code that line reads result.plot(...). Written this way the name resolves, which is what lets the test suite check every name in Part 1 against the live package.

Parameter dot-paths are the other dotted thing here, and they are never capitalised. phases.0.cell.a and instrument.profile.w are data — addresses into the parameter table, not attributes of a class.

Part 1 — Using rietx

The chapters run in the order a first session with the package runs: install it, get one fit to the end, learn what the three objects hold, learn how their parameters are addressed and edited, learn why a fit is staged, run one and control it, read the numbers it returned, read the report on top of them, go back to any state it passed through, find out what is on disk, find the cell when the specimen is unknown, then wire it into something. The closing chapter is the 1.0 stability promise.

Part 1 — Using rietx

• Installation
  • Requirements
  • Optional extras
  • Checking an install
  • Installing from source
  • Validation and accuracy claims
• A first refinement
  • The minimal call
  • refine or a Refinement session
  • Le Bail before Rietveld
  • Worked example: NAC on 11-BM
  • The RefinementResult object
  • Your own data
• Patterns, structures and instruments
  • Every refinable number is a Parameter
  • The pattern
  • The structure
  • The instrument
  • Calibrating an instrument once and reusing it
• The parameter table
  • A dot-path names one scalar
  • Reading the table
  • The three reasons a row is held
  • What the optimiser actually varies
  • Editing the table
  • What a fit reports back
• How a refinement works
  • The parameter groups
  • Why the groups correlate
  • Constraining parameters to each other
  • Restraining a distance or an angle
  • Refinement plans
• Running a refinement
  • Two entry points, and where the settings live
  • Modes: what the intensities are allowed to do
  • Choosing a plan at run time
  • What a stage carries
  • Persisting a plan
  • Running one stage at a time
  • What each stage reports
  • Guards
  • Watching a run
  • Stopping a run
  • What the result records about the run
• Reading the numbers
  • Fit statistics
  • Structure agreement indices
  • The bonding geometry
  • How many observations there are
  • How finely the peaks were sampled
  • What the restraints did
  • What the statistics cannot tell you
  • Diagnostics
• The fit report
  • Building a report
  • Layer 0: statistics independent of the model
  • Layer 1: attributing the misfit
  • Supporting evidence
  • Layer 2: suggested actions
  • Reports at every stage
  • Comparing settings with rietx compare
• The refinement history
  • Switching the history on and off
  • What a node holds
  • Reading a tree
  • Naming a node
  • Going back, and forking
  • Recomputing a node
  • The tree’s identity
• Files and projects
  • Pattern files
  • Structures from CIF
  • Instrument profiles
  • The .rex project directory
  • The history log
  • Exports
• Indexing an unknown cell
  • Picking the peaks
  • Is this list fit to index?
  • Running the search
  • The answer
  • The evidence view
  • From a candidate to a phase
  • The extinction symbol
  • Further reading
• Calling rietx from a program
  • refine_json: one call, five tasks
  • Registering rietx as a tool
  • capabilities()
  • Versioned contracts
  • Further reading: the agent protocol
• Compatibility
  • The data contracts are frozen
  • The Python surface freezes as it is documented
  • Provisional by declaration
  • How a change is classified
  • The JSON the package writes
  • The name and the formats are separate promises
  • What a default promises

Part 2 — Theory

Conventions are stated by physics, never by letters. Rietveld codes disagree on letter assignments (GSAS and FullProf swap the size and strain terms X and Y), on sign conventions (March-Dollase \(r\)), on normalisations (Stephens \(S_{HKL}\), three independent choices), and on whether a table prints a transmission \(A\) or its reciprocal \(A^*\). Wherever a number could be transferred from the literature or from another code, the convention warning sits beside the equation. Transfer a value by matching the physics — the θ-law, the limit, the sign of the effect — never the symbol.

Scope. Constant-wavelength X-ray powder data. Fundamental-parameters profiles, neutron and time-of-flight data, and spherical-harmonics texture are not implemented today. They are planned for v2, behind seams the forward model already carries; nothing in Part 2 describes them.

Part 2 — Theory

• 1. The forward model
  • 1.1. Three intensity models
  • 1.2. The residual row layout
  • 1.3. Discreteness is frozen per stage
• 2. Peak positions
  • 2.1. Lattice metric and Bragg’s law
  • 2.2. Aberration shifts
  • 2.3. Wavelength scales
• 3. Peak profiles
  • 3.1. The instrument ⊕ sample width split
  • 3.2. Thompson-Cox-Hastings pseudo-Voigt
  • 3.3. The true Voigt, via the Faddeeva function
  • 3.4. Finger-Cox-Jephcoat axial divergence
• 4. Intensities
  • 4.1. The species scattering factor
  • 4.2. The structure factor
  • 4.3. Debye-Waller factors and ADP representations
  • 4.4. Anomalous scattering and the powder average
• 5. Intensity corrections
  • 5.1. Lorentz-polarisation
  • 5.2. Attenuation coefficients
  • 5.3. Capillary (cylindrical) absorption
  • 5.4. Flat-plate absorption
  • 5.5. Surface roughness
  • 5.6. Secondary extinction
  • 5.7. Preferred orientation (March-Dollase)
  • 5.8. Quantitative phase analysis and microabsorption
• 6. Microstructure
  • 6.1. Isotropic size and strain
  • 6.2. Stephens anisotropic strain
  • 6.3. Symmetry and the allowed coefficients
  • 6.4. The positivity cone, the seed, and how to read the guard
• 7. Background
  • 7.1. Additive models, never subtraction
  • 7.2. Model-free estimation
  • 7.3. Choosing the flexibility
  • 7.4. Flexibility is a correctness question
• 8. Estimation
  • 8.1. Objective and weights
  • 8.2. Agreement statistics
  • 8.3. Structure agreement indices
  • 8.4. How many observations a pattern holds
  • 8.5. Esds and the Bérar-Lelann inflation
  • 8.6. Esds of derived quantities
  • 8.7. Staged strategy and series
  • 8.8. Solvers
  • 8.9. The fp64 floor
  • 8.10. From fit to report
  • 8.11. Which parameter to free next
• 9. Parameterisation and constraints
  • 9.1. From tree to vector
  • 9.2. Site-symmetry degrees of freedom
  • 9.3. Soft restraints
  • 9.4. Weighting the restraints
• 10. Indexing
  • 10.1. The quadratic form
  • 10.2. The symmetry-allowed subspace
  • 10.3. What a peak list can and cannot support
  • 10.4. Volume from one line
  • 10.5. Figures of merit, in both directions
  • 10.6. Ambiguity, which is reported and not resolved
• 11. Search engines
  • 11.1. Why the search is in \((A \ldots F)\) and not in \((a, b, c, \alpha, \beta, \gamma)\)
  • 11.2. Successive dichotomy
  • 11.3. Index-heuristic trial and error
  • 11.4. What a zone-indexing engine would and would not add
  • 11.5. The obliquity bound is a costed choice
  • 11.6. The reflection ceiling
• 12. Reading a paper against its own numbers
  • 12.1. Rouse b₂: validate against the integral
  • 12.2. Two Coelho papers vs. their own tables
  • 12.3. The FCJ corner: the parameterisation stalls, not the solver
  • 12.4. µR, µt, and why ΔRwp judges none of this

Citing rietx

If rietx contributed to published work, cite [Wu26]. The repository carries the same record as CITATION.cff, which reference managers and GitHub’s “cite this repository” button read directly.

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