Sextet model

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Sextet model specification (Fe-57) — source of truth

Purpose. This document describes exactly how Fitbauer computes the magnetic sextet, so that any other implementation (in particular the web application the program originally grew out of) can reproduce an identical fit. It is the reference contract: if the web follows this document, the same parameters will produce the same absorption and the same transmission.

The canonical implementation lives in core/physics.py, core/constants.py and core/hamiltonian.py. If this document and the code disagree, the code wins.

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1. General conventions

• Velocity axis v in mm/s. The sign is preserved as-is (it may be negative; see folding in §7).

• Transmission model (not absorption): the observed spectrum dips below a baseline. For a single component:

  T(v) = baseline + slope · v − A(v)
  

  where A(v) ≥ 0 is the absorption of the component. With several components the total absorption A_tot = Σ A_c is summed before subtracting (see §6).

• Parameter units: δ (delta), ΔE_Q (quad) and the Γ values in mm/s; BHF in tesla (T); intensities dimensionless; depth dimensionless (absorption scale).

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2. Sextet parameters

Canonical order (see SEXTET_PARAM_NAMES in core/constants.py):

#	Name	Symbol	Meaning
0	delta	δ	Isomer shift (mm/s)
1	quad	ΔE_Q	First-order quadrupole splitting (mm/s)
2	bhf	B_hf	Hyperfine field (T)
3	gamma1	Γ₁	HWHM width of lines 1 and 6 (mm/s)
4	gamma2	Γ₂(rel)	Relative width of lines 2 and 5
5	gamma3	Γ₃(rel)	Relative width of lines 3 and 4
6	depth	d	Depth (global absorption scale)
7	int1	I₁₃	Relative intensity of lines 1,6 with respect to 3,4
8	int2	I₂₃	Relative intensity of lines 2,5 with respect to 3,4
9	int3	I (base)	Base intensity of lines 3,4 (NORMOS convention: fixed to 1)

The six lines are indexed 1..6 from left to right in velocity.

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3. Positions of the six lines (first-order model, historical)

This is the default treatment (treatment="1st_order"), the one the web must replicate.

3.1 Calibration pattern at 33.0 T

The positions come from the published α-Fe velocity standard, NOT from the nuclear moments (see §8). In core/constants.py:

_BASE_POSITIONS = [-10.657, -6.167, -1.677, 1.677, 6.167, 10.657] · 0.5
                = [ -5.3285, -3.0835, -0.8385, 0.8385, 3.0835, 5.3285]   (mm/s)

BHF_DEFAULT_T = 33.0
LINE_POS_33T  = _BASE_POSITIONS              # positions at exactly 33.0 T

⚠️ Do not derive these positions from the nuclear moments. The textbook calculation gives a splitting ~0.4 % smaller (outer line 5.309 vs 5.328 mm/s) and biases the BHF ~0.1 T upwards. The constant 33.0 T is the calibration; an α-Fe spectrum must fit to exactly 33.0 T, just as in NORMOS.

3.2 Effective positions

The positions scale linearly with the field and are shifted by δ and by the quadrupole pattern:

LINE_QUAD_PATTERN = [ +0.5, −0.5, −0.5, −0.5, −0.5, +0.5 ]

position_i = LINE_POS_33T[i] · (BHF / 33.0) + δ + ΔE_Q · LINE_QUAD_PATTERN[i]

That is: the field scales the magnetic splitting, δ shifts the whole sextet, and the first-order quadrupole separates the outer pair (lines 1,6: +ΔE_Q/2) from the rest (lines 2,3,4,5: −ΔE_Q/2).

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4. Intensities and widths of the six lines

4.1 Intensities (relative weights)

i3 = int3                 # lines 3 and 4
i2 = int3 · int2          # lines 2 and 5
i1 = int3 · int1          # lines 1 and 6

weights = [ i1, i2, i3, i3, i2, i1 ]

With the default NORMOS convention (int3 = 1, int2 = 2, int1 = 3) this yields the classic 3 : 2 : 1 : 1 : 2 : 3 pattern.

4.2 Widths (HWHM, half width at half maximum)

gamma2 and gamma3 are relative multipliers applied to gamma1, not absolute widths:

g1 = gamma1               # lines 1 and 6
g2 = gamma1 · gamma2      # lines 2 and 5
g3 = gamma1 · gamma3      # lines 3 and 4

gammas = [ g1, g2, g3, g3, g2, g1 ]

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5. Line profile

Each line contributes weight · profile(v; centre, γ). Two profiles are selectable; the global state lives in core/physics.py (LINE_PROFILE_KIND, VOIGT_SIGMA).

5.1 Lorentzian (default), normalized to peak = 1

L(v; v0, γ) = γ² / ( (v − v0)² + γ² )

γ is the HWHM. L(v0) = 1 at the centre.

5.2 Voigt (optional), normalized to peak = 1

Using the Faddeeva function w(z) (scipy.special.wofz), with σ = VOIGT_SIGMA:

denom = σ · √2
norm  = σ · √(2π)

V(v; v0, γ) = Re[ w( ((v − v0) + iγ) / denom ) ] / norm
peak        = Re[ w( iγ / denom ) ] / norm

profile     = V / peak          # normalized to 1 at the centre

The normalization is analytic at the peak (it does not divide by the discrete maximum over the grid). This avoids underestimating the peak when the velocity grid does not fall exactly on v0. The web must normalize the same way to match.

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6. Total absorption and transmission

6.1 Absorption of a sextet

A_sextet(v) = depth · Σ_{i=1..6}  weights[i] · profile(v; position_i, gammas[i])

6.2 Total transmission model

A_tot(v) = Σ_c  A_c(v)                         # sum over all active components
T(v)     = baseline + slope · v − A_eff(v)

where by default A_eff = A_tot (thin-absorber, linear model). There is an optional thick-absorber / saturation mode with amplitude C = sat_scale > 0:

A_eff(v) = C · ( 1 − exp(−A_tot(v) / C) )       # the C→∞ limit recovers A_eff = A_tot

If the web only implements the thin model, it must use A_eff = A_tot (equivalent to leaving saturation switched off in Fitbauer).

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7. Folding, normalization and velocity axis — CRITICAL

For a fit over the same spectrum to agree, the forward model (§3–§6) is not enough: the data must be folded the same way, normalized the same way, and the velocity axis must be built the same way. If the web folds differently, the BHF, the positions and the areas will come out different even if the sextet model is identical. The canonical implementation is core/folding.py. This section is the part that diverges most between implementations, so it is specified in full.

7.1 What folding is and why

The detector records N channels (typically 512) containing the spectrum twice (forward and backward strokes of the transducer), mirrored about a symmetry centre (the folding point). Folding = averaging each channel with its mirror to obtain N/2 points (typically 256) with a better signal-to-noise ratio. The result is ordered from negative to positive velocity.

7.2 Channel numbering and centre

• Channels are numbered 1..N (1-based), not 0-based. This matters for the formula.
• The center (internal folding point) is the symmetry centre and may be fractional (e.g. 255.77), not just integer or half-integer.
• Relation to Normos: the number Normos reports ("Final/Upper folding point") is usually in full-spectrum convention (≈ 511 for 512 channels) and is approximately twice this GUI's internal centre (≈ 255.5). Conversion in read_normos_folding_point: if the value is ≥ 400 → full spectrum → divide by 2; if < 400 → already a half-spectrum → use as-is.

7.3 Folding algorithm (fold_integer_or_half)

Always produces n_out = N // 2 points. For each point j = 0 .. n_out−1:

distance   = j + 0.5
left_chan  = center − distance
right_chan = center + distance
folded[j]  = 0.5 · ( C(left_chan) + C(right_chan) )

where C(channel) is the 1-based sub-channel linear interpolation (interp_channel_1based):

# channels 1..N, values counts[0..N-1]
if channel < 1:      C = counts[0]   + (channel − 1) · (counts[1]   − counts[0])      # extrapolates
if channel ≥ N:      C = counts[N-1] + (channel − N) · (counts[N-1] − counts[N-2])    # extrapolates
otherwise:
    lo   = floor(channel)
    frac = channel − lo
    if frac ≈ 0:     C = counts[lo−1]
    else:            C = (1 − frac)·counts[lo−1] + frac·counts[lo]

Key to reproducing Normos: folding does NOT stop at integer channel pairs. For fractional centres it uses linear interpolation, and at the edges it extrapolates linearly instead of dropping a channel. That way it always yields N/2 points.

7.4 Folding-point search (find_best_integer_or_half_center)

If it is not supplied by Normos, it is found by minimizing the χ² of the difference between symmetric channels:

1. Candidate grid in steps of 0.5 (by default 250.5 .. 262.5 for 512 channels).
2. For each centre, χ²(center) = Σ (counts[left] − counts[right])² over the pairs.
3. The centre of minimum χ² is taken and the minimum is parabolically interpolated (sub-channel refinement) using the three points around it.

7.5 Edge trimming and normalization (fold_and_normalize)

folded = fold_integer_or_half(counts, center)
# Trims edge_trim channels at each end (1 by default), if the array is large enough:
if edge_trim > 0 and folded.size > 2·edge_trim + 2:
    folded = folded[edge_trim : −edge_trim]

norm  = percentile_90(folded)        # ≈ baseline
y     = folded / norm                # normalized spectrum (~1 at the baseline)
sigma = sqrt( max(folded/2, 1) ) / norm   # normalized Poisson noise

• Edge trimming: the outermost channels of the folded spectrum are less reliable and are discarded (edge_trim = 1 by default). Note it only trims if the array is large enough (> 2·edge_trim + 2); for real 256-point spectra it always applies.
• Normalization: by the 90th percentile of the folded counts (a robust baseline estimator), not by the maximum.
• Poisson σ: sqrt(folded/2) (the /2 comes from averaging two channels) floored at 1 count, divided by norm. These sigma values are the fit weights (see §8).

7.6 Velocity axis (velocity_axis) — do not stretch the scale

full_n   = N // 2
velocity = linspace(−Vmax, +Vmax, full_n)        # build the FULL axis first
# trim the SAME edge positions as in the data:
if edge_trim > 0 and the size matches:
    velocity = velocity[edge_trim : −edge_trim]

⚠️ Classic mistake to avoid: do NOT rebuild the axis as linspace(−Vmax, +Vmax, trimmed_n_points). The full N/2-point axis must be built and then trimmed at the same edges as the data. Rebuilding it with fewer points stretches the velocity scale and biases the BHF.

• Vmax may be negative; the sign is preserved (NORMOS/web compatibility with an inverted axis).

7.7 Numerical folding contract (verifiable)

Reproducible example with core/folding.py. Input: 8 channels (1-based)

counts = [100, 90, 70, 95, 98, 60, 88, 105]

Folding at half-integer centre center = 4.5 → pairs (4,5) (3,6) (2,7) (1,8):

folded = [ 96.5, 65.0, 89.0, 102.5 ]

Folding at fractional centre center = 4.30 (shows the sub-channel interpolation):

folded = [ 93.7, 70.8, 87.2, 101.8 ]

fold_and_normalize(counts, center=4.5, edge_trim=1) (on this small array of 4 folded points, edge_trim does not trim because 4 ≤ 2·1+2):

norm  = 100.7                                          # 90th percentile
y     = [ 0.958292, 0.645482, 0.883813, 1.017875 ]
sigma = [ 0.068979, 0.056612, 0.066245, 0.071091 ]

velocity_axis(N=8, Vmax=4.0, n_points=4, edge_trim=1):

velocity = [ −4.0, −1.333333, +1.333333, +4.0 ]

If the web reproduces these four blocks (to a tolerance of ~1e-6), the folding, the normalization and the axis are identical. Keep this vector as a regression test.

7.8 Reading Normos sidecars (optional)

core/folding.py also reads parameters from associated Normos files to seed the fit (this does not affect the model, only the starting values):

• .RES: final values ISO→δ, BHF, QUA→ΔE_Q, WID (Normos reports FWHM; the internal Lorentzian uses HWHM = FWHM/2!), ARE→depth (via ARE / (π·Γ·Σweights), with Σweights = 2·(3+2+1) = 12).
• .JOB: VMAX, QUA(1).
• .PLT: Vmax from the blocks of 256 values.

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8. Fit objective function (affects the fitted values)

Two implementations can share the forward model and still return different fitted parameters if they minimize different things. Fitbauer (core/fit_engine.py) uses:

• Poisson weights (counts): residual weighted by the variance ≈ counts.
• Non-linear least squares (TRF) with deterministic multistart; optional robust loss and global differential evolution.
• Physical parameter bounds (ranges for BHF, ΔE_Q, etc.).

For a fit identical to Fitbauer's, the web must match: the forward model (§3–§6) and the weighting scheme and the same bounds/seed. If the web only needs the same curve given parameters (simulation), §3–§6 suffice.

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9. Reference vector (verifiable numerical contract)

Values generated by running core/physics.py (Lorentzian profile, first-order mode). Parameters: δ=0, ΔE_Q=0, BHF=33.0, Γ₁=0.300, Γ₂rel=Γ₃rel=1.0, depth=0.02, int1=3, int2=2, int3=1 → weights 3:2:1:1:2:3, baseline=1, slope=0.

Γ₁ = 0.300 is the HWHM value passed to sextet_absorption (equivalent to FWHM = 0.600 mm/s). Mind this distinction: it is the same trap described in §7.8 for the Normos sidecars.

Positions of the 6 lines (mm/s):

[ −5.3285, −3.0835, −0.8385, +0.8385, +3.0835, +5.3285 ]

Sampled absorption and transmission:

v (mm/s)	A(v)	T(v) = 1 − A(v)
−5.3285	0.060236	0.939764
−3.0835	0.040427	0.959573
−0.8385	0.020497	0.979503
0.0	0.001524	0.998476
+0.8385	0.020497	0.979503
+3.0835	0.040427	0.959573
+5.3285	0.060236	0.939764

If the web implementation reproduces this table (to a tolerance of ~1e-6), the forward sextet model is identical. It is worth keeping this vector as a regression test on both sides.

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10. Advanced treatments (optional)

By default the web only needs the first order (§3). For completeness, core/physics.py + core/hamiltonian.py offer two further quadrupole treatments, by diagonalizing the Hamiltonian ω_e·I_z + (ΔE_Q/6)(3 I_{z'}² − I(I+1)) (axial EFG, η=0):

• kundig_fixed: fixed angle β between B and V_zz.
• kundig_powder: polycrystalline average by Gauss–Legendre quadrature over n_quad orientations (β ∈ [0, π]).

Only replicate these if the web is going to offer those modes.

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11. Checklist for aligning the web

1. Base α-Fe positions at 33.0 T = ±0.8385 / ±3.0835 / ±5.3285 mm/s (§3.1).
2. Linear scaling · (BHF/33.0), shift +δ, quadrupole pattern [+0.5,−0.5,−0.5,−0.5,−0.5,+0.5]·ΔE_Q (§3.2).
3. Intensities [i1,i2,i3,i3,i2,i1] with i1=int3·int1, i2=int3·int2, i3=int3 (§4.1).
4. Widths gamma2/gamma3 as multipliers of gamma1 (§4.2).
5. Lorentzian with peak = 1 (or Voigt with analytic peak normalization) (§5).
6. Transmission baseline + slope·v − A_tot; optional saturation (§6).
7. Folding (§7) — only if comparing over data:
   • 1-based channels; possibly fractional symmetry centre (§7.2).
   • Normos folding-point conversion (≈ twice the internal centre) (§7.2).
   • Folding 0.5·(C(center−(j+0.5)) + C(center+(j+0.5))) with sub-channel linear interpolation and edge extrapolation (§7.3).
   • Edge trimming edge_trim=1 (§7.5).
   • Normalization by the 90th percentile and σ = sqrt(max(folded/2,1))/norm (§7.5).
   • Velocity axis built in full and then trimmed, not rebuilt with fewer points (§7.6).
   • Reproduce the numerical folding contract (§7.7).
8. Same Poisson weighting scheme (the σ of §7.5) and bounds — only if the same fit is required, not just the same curve (§8).
9. Reproduce the forward-model reference vector of §9 as a test.

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12. What is needed to produce a concrete "what to change" for the web

This document is the specification of the Fitbauer side. To deliver an exact delta (which lines to change in the web) it helps to have:

• The current web code that computes the sextet (formulas for positions, intensities, profile, transmission) and the language/stack (JS, PHP, Python…).
• If it exists, the reference field value the web uses (32.95 T? 33.0 T?) and its base positions — this is the most likely cause of the historical discrepancy.
• A test spectrum (e.g. α-Fe) fitted on both sides to compare numbers.