Fit templates

A template is a YAML file with one or more regions. It is validated before any fitting happens, so a typo fails with a precise message instead of a strange fit.

name: Te3d                 # used in reports and file names
version: "1"
description: Tellurium 3d: telluride / Te0 and Te(IV) oxide doublets.
source: Moulder et al. 1992; NIST SRD 20      # where the numbers come from, in words
references: [moulder1992, nist_srd20]        # bibliography keys (elements/data/bibliography.yaml)
regions:
  - label: Te 3d           # matched against spectrum labels ("Te 3d", "Te3d")
    element: Te
    orbital: 3d
    window: [568.0, 592.0] # binding-energy range that is fitted (eV)
    background: shirley    # shirley | tougaard | linear | active_shirley | none
    background_params: {}  # e.g. {fit_B: true} for tougaard, {n_avg: 7} for shirley
    lineshape: pseudo_voigt  # default for components: pseudo_voigt | gl_product | voigt |
                             # gaussian | lorentzian | doniach_sunjic | exp_tail
    default_shape:
      eta: {value: 0.3, min: 0.1, max: 0.7}   # shape parameters shared by default
    fwhm_tolerance: 0.15   # optional: every width within ±15 % of the first component's
    rsf_line: Te 3d5/2     # line whose (whole-doublet) sensitivity factor is used
    components:
      - name: Te-M
        chemical_state: telluride / metallic Te
        provenance: {source: bahl1978, method: literature}   # see docs/constraints.md
        center: {value: 572.8, min: 571.8, max: 573.6}
        fwhm:   {value: 1.0,   min: 0.6,   max: 1.6}
        area:   {min: 0}                 # initial area is guessed from the data
        doublet:
          splitting: 10.39               # minor line at center + splitting
          ratio: 0.6667                  # minor / major area
          splitting_vary: false          # optionally free within ±splitting_tolerance
          share_fwhm: true
      - name: Te(IV)
        enabled: true                    # disabled components are kept but not fitted
        center: {expr: "{Te-M.center} + 3.3"}   # tie to another component
        fwhm:   {expr: "{Te-M.fwhm} * 1.25"}
        doublet: {splitting: 10.39, ratio: 0.6667}

Parameters

Each of center, fwhm, area and the shape parameters takes value, min, max, vary and expr. An expr uses lmfit syntax, where {Component.param} refers to another component's parameter. Expressions are resolved after all components are created, so forward references work.

Lineshapes and their shape parameters

Getting a starting template

xpsflow propose data/sample.vms "sample/Se 3d" --out templates/Se3d_mine.yaml

This proposes components from the detected peaks and assigns them to literature chemical states that are plausible for the elements found on the sample. Edit it, then run with xpsflow run data/ --template templates/Se3d_mine.yaml.

Provenance

Every component may carry provenance: {source, method, note}. source is a bibliography key; method is one of literature, instrument, user, data or default. Components without a block inherit the region's provenance, then the template's first reference. Components xpsflow proposes itself are marked data. The report prints the full table; see docs/constraints.md.

Reproducibility

Every run writes the exact regions it used, after model selection, to templates/ next to the report, so the analysis can be repeated or reviewed without the original session.