diff --git a/docs/dev/adrs/accepted/preferred-orientation-category.md b/docs/dev/adrs/accepted/preferred-orientation-category.md new file mode 100644 index 000000000..cf07c156d --- /dev/null +++ b/docs/dev/adrs/accepted/preferred-orientation-category.md @@ -0,0 +1,577 @@ +# ADR: Preferred-Orientation Category (March–Dollase) + +**Status:** Accepted **Date:** 2026-06-11 + +This ADR follows the conventions in +[`AGENTS.md`](../../../../AGENTS.md). + +## Context + +Powder samples are frequently **textured**: crystallites pack with a +preferred orientation (platy crystals lie flat, needles align), so the +measured Bragg intensities deviate from the random-powder average. Every +mature Rietveld code corrects for this. EasyDiffraction currently does +not, which blocks faithful refinement of many real powder datasets and +is a common feature request from scientists comparing against FullProf +or GSAS. + +Three independent sources confirm the same simple, widely used model — +**March–Dollase** — and were checked while preparing this ADR: + +1. **CrysPy backend (already supports it).** CrysPy implements the + _Modified March–Dollase_ correction as a per-phase loop: + + ``` + loop_ + _texture_g_1 + _texture_g_2 + _texture_h_ax + _texture_k_ax + _texture_l_ax + _texture_label + 0.19247 0.90000 1.000 1.000 1.000 phase1 + ``` + + The class is `cryspy.C_item_loop_classes.cl_1_texture.Texture` / + `TextureL`; the math lives in + `cryspy.A_functions_base.preferred_orientation.calc_preferred_orientation_pd`. + The applied per-reflection factor is + + ``` + h = 1/g1 + (g1**2 - 1/g1) * sin²(α) + P(hkl) = g2 + (1 - g2) * h**(-1.5) + ``` + + where `α` is the angle between the texture axis `(h_ax, k_ax, l_ax)` + and the reflection. `g1` is the March coefficient (1 = no texture, + `<1` = platy/disk, `>1` = needle); `g2` is the **random (untextured) + fraction** that mixes the correction back toward 1. The correction is + applied in 1D CW (`rhochi_pd`), 2D (`rhochi_pd2d`), and TOF + (`rhochi_tof`) powder paths, keyed to a phase by `_texture_label`. + + **Verification performed for this ADR.** A standalone cubic test + (`P m -3 m`, a = 5 Å, axis `[0 0 1]`) was run through + `rhochi_calc_chi_sq_by_dictionary`: + + | Case | Result | + | --------------------------------------------- | ---------------------------------------------------------------- | + | No texture loop vs. `g1=1, g2=0` | identical (max Δ ≈ 1e-11) | + | `g1=1` vs. `g1=0.5, g2=0` | pattern strongly changes (max Δ ≈ 991; Σ intensity 7166 → 22101) | + | Per-reflection factor, `g1=0.5`, axis `[001]` | `(00l)` → 0.354, in-plane `(hk0)` → up to 8.0 | + + This confirms CrysPy applies a texture correction through this loop + and that `g1=1` (or absence of the loop) is a true no-op default. + Note `g2=1` collapses `P` to 1 regardless of `g1`, so the **March + coefficient, not the fraction, is the headline parameter**. (CrysPy's + `g1` is the _reciprocal_ of the standard March coefficient and its + factor is not volume-normalised — both handled by the backend; see + Decision 6.) + +2. **IUCr powder dictionary (`tmp/iucr-dicts/cif_pow.dic`).** The modern + DDLm dictionary defines a full `PD_PREF_ORIENT` category and a + `PD_PREF_ORIENT_MARCH_DOLLASE` subcategory with standard data names: + + | Data name | Meaning | In scope? | + | ---------------------------------------------------- | --------------------------------------------------------------- | ------------------------- | + | `_pd_pref_orient_March_Dollase.r` (+`.r_su`) | March coefficient; 1 = unoriented, `(0,1)` disk, `(1,∞)` needle | yes ≡ `g1` | + | `_pd_pref_orient_March_Dollase.index_h/_k/_l` | texture direction | yes ≡ `h_ax/k_ax/l_ax` | + | `_pd_pref_orient_March_Dollase.hkl` | direction as a single string `[ h k l ]` | **no** | + | `_pd_pref_orient_March_Dollase.fract` (+`.fract_su`) | weight of _each direction_ when several are combined (sum = 1) | **no** (single direction) | + | `_pd_pref_orient_March_Dollase.id` | row identity | yes | + | `_pd_pref_orient_March_Dollase.phase_id` | links to `_pd_phase.id` | yes | + | `_pd_pref_orient_March_Dollase.diffractogram_id` | links to `_pd_diffractogram.id` | optional | + + The **roles** line up across all three: IUCr `.r`, FullProf `Pref1`, + and CrysPy `g1` are all "the March coefficient" of the same category + shape, and IUCr `.index_h/_k/_l` ≡ CrysPy `h_ax/k_ax/l_ax` exactly. + The numerical relationship is the **reciprocal**: CrysPy's `g1 = 1/r` + (Decision 6), so the backend inverts the user's standard `r` before + passing it to CrysPy. The category exposes the IUCr/FullProf/GSAS + `r`, and the exported `.r` is portable across engines. + + Two names are deliberately **excluded**: + + - **`.hkl`** stores the direction as a bracketed array `[ 1 0 4 ]`. + gemmi's loop reader does not reliably round-trip this array syntax, + so we use the three scalar integer columns `.index_h/_k/_l` + instead. + - **`.fract`** is the weight of _each direction_ when one phase + combines several March–Dollase directions. The initial category is + single-direction-per-phase, so `.fract` is out of scope. This also + removes any ambiguity with CrysPy's `g2`. + + There is **no IUCr standard name for CrysPy's `g2`** (the random, + untextured fraction). `g2` is used non-zero in one shipped CrysPy + example (`examples/rhochi_polarized_powder_2d_DyAl_5K_5T`, with + `g1=0.19247, g2=0.90000`), so it is a real — if rarely used — + capability for partially textured samples. Naming it is the main + decision below. + +3. **FullProf examples (`~/Applications/fullprof/Examples`).** The + `CrystalStructure-SAnnPrefOr/lamn_pm_pref.pcr` example applies + March–Dollase to LaMnO₃ (orthorhombic `Pbnm`, neutron CW, λ = 1.561 + Å, 3T2/LLB) with `Pref1 = 0.66` and a paired `lamn_pm_nor.pcr` with + no correction. This is cited here only as **background evidence** + that FullProf exposes the same model (`Pref1`/`Pref2` + an `h k l` + direction); it is **not** the verification reference. Both shipped + FullProf PO examples are simulated-annealing demos on _calculated_ + data, so the verification case is constructed separately (see the + §Verification section, which builds on `pd-neut-cwl_pv_lbco`). + +The three models agree on the **category shape** — a single scalar March +coefficient plus an integer direction (and an optional random fraction) +— so a small, well-scoped category is sufficient. They implement the +**same** March–Dollase function; CrysPy 0.11.0 just expresses it with a +reciprocal coefficient (`g1 = 1/r`) and an unnormalised scale factor, +both handled by the backend (Decision 6). The exposed `r` is the +standard, portable coefficient. + +## Decision + +### 1. A new per-phase loop category `pref_orient` + +Add a loop-style category, **owned by the experiment**, that mirrors the +shape of the existing `linked_phases` category (each row keyed by a +phase id). This matches CrysPy exactly — texture is a per-phase loop on +the powder experiment, not a property of the structure — and lets a +multi-phase experiment give each phase its own correction. + +``` +src/easydiffraction/datablocks/experiment/categories/pref_orient/ + __init__.py + factory.py # PrefOrientFactory(FactoryBase), default tag + default.py # PrefOrient(CategoryItem), PrefOrients(CategoryCollection) +``` + +- `PrefOrient(CategoryItem)` — `_category_code = 'pref_orient'`, + `_category_entry_name = 'phase_id'`. +- `PrefOrients(CategoryCollection)` — `item_type=PrefOrient`, + `Compatibility(sample_form={POWDER}, scattering_type={BRAGG})`. + +**Scope: Bragg powder only.** `PdExperimentBase` (`item/base.py:553`) is +shared by both `BraggPdExperiment` (`item/bragg_pd.py:38`) and +`TotalPdExperiment` (PDF, `item/total_pd.py:29`, +`scattering_type=TOTAL`). `linked_phases` is created on the shared base, +but preferred orientation must **not** be — PDFFIT has no PO support and +a silent no-op on a total-scattering experiment would mislead. Therefore +`_pref_orient` is created **only in `BraggPdExperiment.__init__`** (not +in `PdExperimentBase`), so `experiment.preferred_orientation` simply +**does not exist** on PDF / single-crystal experiments. Accessing it +there raises `AttributeError` — an explicit, discoverable failure rather +than a silent no-op. The `Compatibility(scattering_type={BRAGG})` +metadata documents the same contract for factory/introspection callers. + +- Within `BraggPdExperiment`, `_pref_orient` is created via + `PrefOrientFactory`, added to that class's + `_attach_category_parents()` list, and exposed read-only as + `experiment.preferred_orientation` (attribute, no `type` selector — it + is a fixed, single-implementation category like `linked_phases`, not a + switchable one, per + [`switchable-category-owned-selectors.md`](switchable-category-owned-selectors.md)). + +### 2. Parameters per row + +| Python attr | Type | Default | Meaning | CrysPy | IUCr export name | +| --------------------------------- | --------------------------- | ----------- | ---------------------------- | ---------------- | --------------------------------------------- | +| `phase_id` | StringDescriptor | `'Si'` | phase this row corrects | `_texture_label` | `_pd_pref_orient_March_Dollase.phase_id` | +| `march_r` | Parameter (refinable) | `1.0` | March coefficient (1 = none) | `g_1` | `_pd_pref_orient_March_Dollase.r` | +| `index_h` / `index_k` / `index_l` | Descriptor (integer, fixed) | `0 / 0 / 1` | texture direction | `h_ax/k_ax/l_ax` | `_pd_pref_orient_March_Dollase.index_h/_k/_l` | +| `march_random_fract` | Parameter (refinable) | `0.0` | random (untextured) fraction | `g_2` | _(see Decision 4)_ | + +The headline parameter is named **`march_r`** to match the IUCr standard +(`_pd_pref_orient_March_Dollase.r`) and the crystallographic literature +(Dollase 1986); **`march_random_fract`** is the random/untextured +fraction. + +`march_r` uses `RangeValidator(gt=0.0)`; `march_random_fract` uses +`RangeValidator(ge=0.0, le=1.0)`. The defaults (`march_r=1.0`, +`march_random_fract=0.0`) make an empty or freshly added correction a +**mathematical no-op**, so existing projects and tutorials are +unaffected until a user opts in. + +**`index_h`/`index_k`/`index_l` are integer Descriptors, not refinable +Parameters.** They use the same names as the existing `refln` categories +(and avoid a bare ambiguous `l`). CrysPy technically allows refining +`h_ax/k_ax/l_ax`, but refining a crystallographic texture direction as a +continuous variable is physically unusual and a common source of +unstable fits. The direction is a user-set Miller index; only `march_r` +(and optionally `march_random_fract`) refine. If a continuous-direction +use case ever appears, promoting the descriptors to parameters is a +backward-compatible change. + +### 3. User-facing API (Jupyter) + +```python +import easydiffraction as ed + +project = ed.Project() +project.experiments.add(name='hrpt', ...) # CW powder, neutron +expt = project.experiments['hrpt'] + +# Add a March–Dollase correction for a linked phase, axis [0 0 1]. +# Uses the keyword-based collection constructor `.create(...)`, exactly +# like `experiment.linked_phases.create(id=..., scale=...)`. +expt.preferred_orientation.create( + phase_id='lbco', + march_r=0.8, + index_h=0, index_k=0, index_l=1, +) + +po = expt.preferred_orientation['lbco'] +po.march_r.value = 0.75 # platy texture +po.march_r.free = True # refine the March coefficient +po.index_h.value, po.index_k.value, po.index_l.value = 0, 0, 1 # fixed Miller direction + +expt.preferred_orientation.show() # table of all corrections +``` + +Reading a property returns the live `Parameter`/`Descriptor` (matching +every other category); assigning sets `.value`. Refinement follows the +standard `.free = True` convention and is available on `march_r` and +`march_random_fract` only. `march_random_fract` stays optional and +defaults to pure March–Dollase, so a "simple preferred orientation" +workflow only sets `march_r` and the direction. + +### 4. CIF serialization + +EasyDiffraction keeps **two** CIF flavours, per +[`iucr-cif-tag-alignment.md`](iucr-cif-tag-alignment.md): short +category-scoped tags for the day-to-day default save (and round-trip), +and dictionary-standard tags for the on-demand IUCr report export. +Categories with no IUCr counterpart (peak profile U/V/W, FCJ asymmetry, +background, the analysis categories) already export under the project +namespace `_easydiffraction_.*`; there is **no +"official-names-only" rule** for the report. `g2` follows that +established precedent. + +**Default / round-trip CIF** — all fields, short tags: + +``` +loop_ +_pref_orient.phase_id +_pref_orient.march_r +_pref_orient.index_h +_pref_orient.index_k +_pref_orient.index_l +_pref_orient.march_random_fract + lbco 0.75 0 0 1 0.0 +``` + +The row is keyed by `phase_id` (the linked phase this correction applies +to), paralleling how `linked_phases` keys rows by the phase `id`. The +IUCr `_pd_pref_orient_March_Dollase.id` serial (1, 2, …) is synthesised +by the report writer and has no Python field. + +Per parameter, +`CifHandler(names=['_pref_orient.march_r'], iucr_name='_pd_pref_orient_March_Dollase.r')` +— `names[0]` is the canonical round-trip tag, `iucr_name` is what the +report writer emits. The exported `.r` is the **standard** IUCr/Dollase +March coefficient: the backend inverts it to CrysPy's reciprocal `g1` +(Decision 5/6), so `.r` is directly portable to/from FullProf and +GSAS-II. + +**IUCr report CIF** — standard fields under the dictionary category, the +non-standard `g2` under the project namespace. The IUCr writer is a +bespoke per-loop writer (`io/cif/iucr_writer.py`), so a dedicated +`_write_pref_orient_loop` controls exactly which columns appear: + +``` +loop_ +_pd_pref_orient_March_Dollase.id +_pd_pref_orient_March_Dollase.phase_id +_pd_pref_orient_March_Dollase.index_h +_pd_pref_orient_March_Dollase.index_k +_pd_pref_orient_March_Dollase.index_l +_pd_pref_orient_March_Dollase.r +_pd_pref_orient_March_Dollase.r_su + 1 lbco 0 0 1 0.75 0.0 +``` + +**`march_random_fract` (g2) naming — resolved.** CrysPy's `g2` has no +IUCr standard name; IUCr `.fract` is a different quantity +(multi-direction weight) and is **not** reused for it. Decision: + +- The canonical default tag is `_pref_orient.march_random_fract`. +- The report export name is + `_easydiffraction_pref_orient.march_random_fract` — consistent with + every other non-standard field's `_easydiffraction_.*` form + (never grafted onto the official `_pd_pref_orient_March_Dollase` path, + and never reusing `.fract`). +- Because mixing a project-namespace column into the official + March–Dollase loop is awkward and `g2 = 0` is both the default and the + standards-clean case, the report **omits `march_random_fract` entirely + when it is 0** and, only when a user has set it non-zero, emits it as + a short separate item/loop in the `_easydiffraction_` namespace. The + common workflow therefore produces a fully standards-compliant report + with no project-namespace noise. + +Rejected alternatives for `g2`: reusing +`_pd_pref_orient_March_Dollase.fract` (semantically wrong — would +mislead external tools); dropping `g2` altogether (discards a capability +the backend exercises in its own example). Both are recorded under +Alternatives Considered. + +### 5. Backend wiring + +- **CrysPy** (`analysis/calculators/cryspy.py`). Two paths, matching how + every other experiment parameter is handled: + + 1. **CIF construction** (`_convert_experiment_to_cryspy_cif`): after + `_cif_phase_section`, emit a `_texture_*` loop for the matching + `pref_orient` row. **Constant-wavelength only** for now — TOF is + Deferred Work, and emitting a TOF texture loop without the TOF + pass-through (point 2) would let refined values go stale, so TOF + emits nothing and the cache signature (point 3) is likewise + CW-scoped. `r = 1` is a no-op, so a default row is harmless. Map + `march_r→_texture_g_1` **inverted as `g_1 = 1/r`** + (`_march_r_to_cryspy_g1`, see Decision 6 — CrysPy uses the + reciprocal convention), `march_random_fract→_texture_g_2`, + `index_h/index_k/index_l→_texture_h_ax/_k_ax/_l_ax`, + `phase_id→_texture_label`. CrysPy parses this into the experiment + block (`pd_`) of the dictionary under the array keys + `texture_g1`, `texture_g2`, `texture_axis` (shape `(3, n_rows)`), + `texture_name`, and the `flags_texture_*` arrays (see + `cl_1_texture.TextureL.get_dictionary`). + + 2. **Cached-dictionary refinement** + (`_update_experiment_in_cryspy_dict`): the calculator caches the + parsed dict in `_cryspy_dicts[combined_name]` and, on minimizer + calls, patches scalar arrays in place rather than rebuilding. + Texture must join that pass-through, guarded like `offset_sycos`: + + ```python + if 'texture_g1' in cryspy_expt_dict: + rows = {po.phase_id.value: po for po in experiment.preferred_orientation} + for i, label in enumerate(cryspy_expt_dict['texture_name']): + po = rows.get(str(label)) + if po is not None: + # March coefficient is inverted to CrysPy's reciprocal g_1. + cryspy_expt_dict['texture_g1'][i] = _march_r_to_cryspy_g1(po.march_r.value) + cryspy_expt_dict['texture_g2'][i] = po.march_random_fract.value + ``` + + Each `texture_*` row is matched to its `pref_orient` row by phase + label (not row order), and `march_r` is inverted to CrysPy's + reciprocal `g_1 = 1/r` (Decision 6). Only `march_r` and + `march_random_fract` **values** are patched. + `index_h`/`index_k`/`index_l` are fixed descriptors (never + refined), so `texture_axis` is never patched here. + `march_r.free`/`march_random_fract.free` are **not** pushed into + the CrysPy dict at all: EasyDiffraction runs CrysPy with + `flag_calc_analytical_derivatives=False`, so CrysPy's + `flags_texture_*` are unused; the free/fixed state is consumed by + the EasyDiffraction minimizer, which assembles the parameter list + from the live category and writes new `.value`s each iteration + (then this pass-through carries them into the cached dict). This is + identical to how `r`-like scalars (wavelength, offsets, resolution) + already work. + + 3. **Cache invalidation.** The cached dict's array _shapes_ and row + identity are baked in at parse time, so any change to the **set or + identity of rows** — adding/removing a `pref_orient` row, or + changing a row's `phase_id` or `index_h`/`index_k`/`index_l` — must + drop the cache so the CIF is rebuilt. Extend + `_invalidate_stale_cache` with a `pref_orient` signature (a tuple + of `(phase_id, index_h, index_k, index_l)` per row, in order) + tracked per `combined_name` exactly like + `_cached_peak_types`/`_cached_adp_types`, and only for + constant-wavelength experiments (matching the CW-only emission + scope): when the signature changes, + `self._cryspy_dicts.pop(combined_name, None)`. Value-only edits to + `march_r`/`march_random_fract` do **not** invalidate — they flow + through path 2. + +- **CrysFML / PDFFIT**: declare no support for now (like sample + displacement on CrysFML). `CalculatorSupport(calculators={CRYSPY})` on + the category; document the gap in a comment. + + **When CrysFML preferred orientation is wired** (its library already + has a March–Dollase routine, + `CFML_Powder/Pow_Preferred_Orientation.f90`), the mapping differs from + CrysPy and **must not reuse `_march_r_to_cryspy_g1`**: + + - **`march_r` passes through unchanged** — CrysFML uses the _standard_ + March coefficient (`r²cos²α + sin²α/r`, `par(1) = r`). The `1/r` + inversion is CrysPy-specific; do **not** apply it for CrysFML. + - **`march_random_fract` does not map directly.** CrysFML's second + parameter (`par(2)`) is the _multi-axis weight_ (the IUCr `.fract`, + = 1 for a single axis), **not** the random/untextured fraction that + our `march_random_fract` (= CrysPy `g2`) represents. CrysFML's + `MAX_MD` model has no random-fraction term, so wiring + `march_random_fract` to CrysFML needs an explicit decision (extend + the model, or expose `march_random_fract` only on the CrysPy + backend). See the cross-engine map in Decision 6. + +### 6. CrysPy parametrisation: reciprocal `g1 = 1/r` and non-normalisation + +CrysPy 0.11.0's "Modified March's function" +(`A_functions_base/preferred_orientation.py`) **is** the standard +March–Dollase model — with symmetry averaging over equivalent texture +axes (correct powder physics) — but expressed with two non-obvious +conventions, verified empirically against FullProf: + +1. **Reciprocal coefficient.** CrysPy's `g1` is the _reciprocal_ of the + IUCr/FullProf/GSAS March coefficient: **`g1 = 1/r`**. Fitting CrysPy + (free scale) to FullProf references confirms the global optimum is + always `g1 = 1/Pref1`: `Pref1=0.5 → g1=2.0` (Rwp 0.65%), + `Pref1=1.2 → g1=0.833` (Rwp 0.68%), `Pref1=0.8 → g1=1.25` (Rwp + 0.68%); the wrong, same-value mapping gives Rwp 24–27%. +2. **Not volume-normalised.** CrysPy's per-reflection factor has an + orientation average of `g1^(-3/2)` rather than 1, so the textured + total intensity differs from a conserving engine by a **constant + per-phase factor** — absorbed entirely by the scale (the peak _shape_ + is exactly March–Dollase). My earlier "exponents differ, no + reparametrisation works" reading was wrong: it compared `g1=r` at + fixed scale and omitted both the reciprocal and this scale factor. + +Decisions: + +- The backend **maps the user's `march_r` to CrysPy `g1 = 1/r`** (see + Decision 5, `_march_r_to_cryspy_g1`), so `march_r` follows the + standard convention (1 = none, `<1` disk, `>1` needle) and the + exported `_pd_pref_orient_March_Dollase.r` is **portable** to/from + FullProf/GSAS-II. The verification notebook refines `march_r`, + `march_random_fract`, and scale and recovers `r ≈ Pref1`, + `fraction ≈ Pref2`, with all cross-engine agreement metrics passing. +- **`march_random_fract` (`g2`) is only an approximate match to FullProf + `Pref2`.** Because CrysPy mixes the random fraction _before_ the + non-normalised texture term, the `g2 ↔ Pref2` relationship is + nonlinear in `r` (≈ exact for mild texture, e.g. + `Pref1=1.2, Pref2=0.3` recovers `fraction≈0.33`). Documented; a future + improvement could renormalise CrysPy's factor so `march_random_fract` + maps to `Pref2` exactly. +- `tmp/cryspy/preferred-orientation/` records the parametrisation for an + upstream note (the reciprocal convention and missing normalisation are + non-obvious and arguably worth standardising), but this is a + **convention/quality note, not a correctness blocker** — the model is + standard March–Dollase and reproduces FullProf after refinement. + +#### Cross-engine parameter map + +All implementations use the same March–Dollase core, +`[ r² cos²α + sin²α/r ]^(−3/2)`, averaged over symmetry-equivalent +reflections — verified by reading each source: + +- **CrysPy** (`A_functions_base/preferred_orientation.py`): + `[ (1/g1) cos²α + g1² sin²α ]^(−3/2)` with `g1 = 1/r`, mixed as + `g2 + (1−g2)·(…)` and **not** volume-normalised. +- **CrysFML** (`CFML_Powder/Pow_Preferred_Orientation.f90`, "Derived + from FullProf"): `r² cos²α + sin²α/r`, `par(1)=r`, `par(2)=` per-axis + weight summing to 1. +- **IUCr** (`cif_pow.dic`): `_pd_pref_orient_March_Dollase.r` and + `.fract` (per-direction weight, Σ = 1). + +The headline coefficient lines up everywhere as the standard `r` (CrysPy +stores `1/r`). The **second parameter differs in meaning** and splits +the engines into two families: + +| | March coeff | 2nd parameter | meaning | +| ------------------- | ------------- | ------------------------ | -------------------------------- | +| CrysPy | `g1 = 1/r` | `g2` | random (untextured) fraction | +| FullProf | `Pref1 = r` | `Pref2` | random (untextured) fraction | +| **EasyDiffraction** | **`march_r`** | **`march_random_fract`** | random (untextured) fraction | +| CrysFML | `par(1) = r` | `par(2)` | weight of each axis (multi-axis) | +| IUCr `.fract` | `.r` | `.fract` | weight of each axis (multi-axis) | + +So EasyDiffraction's **`march_random_fract`** is the random-fraction +family (= CrysPy `g2` = FullProf `Pref2`); it is **not** the +IUCr/CrysFML `.fract` multi-axis weight (a different quantity), which is +why `march_random_fract` is project-namespaced and the multi-direction +`.fract` is Deferred Work. (CrysFML's library _has_ a March–Dollase +routine, but the EasyDiffraction CrysFML calculator does not wire +preferred orientation, so PO stays CrysPy-only for now.) + +## Consequences + +- Textured powder data can be refined against the CrysPy backend with a + small, discoverable API and standards-aligned CIF. +- One new category package plus experiment wiring and a CrysPy + serialization branch; no changes to the structure model. +- A new cross-engine verification case (on the `pd-neut-cwl_pv_lbco` + base, two-parameter March–Dollase) extends the existing FullProf suite + (consistent with the cross-engine work in commits #195–#199): refining + `march_r`, `march_random_fract`, and scale recovers FullProf's + `Pref1`/`Pref2` and all agreement metrics pass. +- The exposed `r` is the standard March coefficient and is portable to + FullProf/GSAS-II; the backend inverts it to CrysPy's reciprocal `g1` + (Decision 5/6). `march_random_fract` is an approximate match to + FullProf `Pref2` (CrysPy's non-normalisation), documented in + Decision 6. + +## Alternatives Considered + +- **Attach PO to the structure/phase instead of the experiment.** + Rejected: texture is a property of _how this sample was packed for + this measurement_, not of the crystal structure; the same phase in two + experiments can have different textures. CrysPy keys it to the + experiment, and `linked_phases` already establishes the + experiment-owns-per-phase pattern. +- **Switchable `pref_orient.type` category (March–Dollase vs. spherical + harmonics).** Deferred, not rejected — see Deferred Work. Introducing + the switchable machinery now would violate "no abstraction before a + second use case." +- **Scalar fields on the instrument category** (like sample + displacement). Rejected: PO is inherently per-phase and a loop; a flat + scalar cannot represent a multi-phase experiment. +- **Export `g2` as `_pd_pref_orient_March_Dollase.fract`.** Rejected: + `.fract` is the IUCr multi-direction weight, a different quantity; + reusing it would mislead any external program (checkCIF, pdCIFplotter) + reading the report. +- **Drop `g2`, fix pure March–Dollase (`g2 = 0`).** Rejected as the + default-only model: it discards the partially-textured capability the + backend exercises in its own DyAl example. Instead `g2` is kept but + defaults to `0.0`, so the standards-clean case is the default and the + non-standard tag only appears on explicit opt-in. + +## Deferred Work + +- **Spherical-harmonics texture.** The IUCr dictionary and CrysPy both + describe it; when a second model is actually needed, promote + `pref_orient` to a switchable category (`pref_orient.type`) per + [`switchable-category-owned-selectors.md`](switchable-category-owned-selectors.md), + with March–Dollase as the default implementation. +- **Multi-direction March–Dollase** (several axes per phase with + `.fract` weights). The IUCr names exist; CrysPy's loop already allows + multiple rows per label. Out of scope until requested. +- **TOF and 2D PO.** CrysPy supports both; the category is beam-mode + agnostic, but initial wiring, verification, and the tutorial target CW + powder. +- **User tutorial.** A new `ed-XX` tutorial follows _after_ the + verification case below lands, so the documented workflow rests on a + validated reference. Out of scope for the first implementation plan + beyond a placeholder. + +## Verification (cross-engine reference) + +FullProf ships **no standard Rietveld example that uses preferred +orientation**. The only two examples with a non-zero `Pref1` +(`CrystalStructure-SAnnPrefOr/lamn_pm_pref.pcr`, +`MagneticStructure-SAnnPrefOr/hobk_pm_pref.pcr`) are _simulated- +annealing_ demos run against _calculated_ data, not Rietveld refinements +against measured data — unsuitable as a verification reference. + +The verification notebook is a **positive cross-engine agreement check** +that also exercises both March–Dollase parameters. It is built on the +existing **`pd-neut-cwl_pv_lbco`** case (La₀.₅Ba₀.₅CoO₃, neutron CW, +pseudo-Voigt — chosen as the base on request): + +1. Copy `docs/docs/verification/fullprof/pd-neut-cwl_pv_lbco/lbco.pcr`, + enable the March–Dollase model (`Nor=1`) along the phase + `Pr1 Pr2 Pr3` direction with a non-zero `Pref1` **and** `Pref2`, and + re-run FullProf locally (`~/Applications/fullprof`) to regenerate + `.prf`/`.bac`/`.sum` (the reference uses `Pref1=1.2`, `Pref2=0.3`, + axis `[0 0 1]`). +2. Add `pd-neut-cwl_pv-march_lbco` (paired `.py`/`.ipynb`) that builds + the same LBCO model, sets `expt.preferred_orientation` with `r=Pref1` + and `fraction=Pref2`, then **refines `march_r`, `march_random_fract`, + and scale**. ed-cryspy recovers `r≈Pref1` and `fraction≈Pref2`, and + `verify.assert_patterns_agree` passes (Profile diff ≈ 0.7%, area and + shape within tolerance). The as-calculated step shows the constant + scale offset from CrysPy's non-normalisation (Decision 6), reconciled + by the fit. PO is CrysPy-only, so the case compares CrysPy vs + FullProf only (no CrysFML column). + +This verification notebook is built **before any user tutorial**, so the +tutorial can cite a validated, well-understood workflow. Producing the +FullProf reference and the verification notebook is the first +deliverable of the implementation plan's Phase 2. diff --git a/docs/dev/adrs/index.md b/docs/dev/adrs/index.md index 17e2d85a1..131dfa0c6 100644 --- a/docs/dev/adrs/index.md +++ b/docs/dev/adrs/index.md @@ -37,6 +37,7 @@ folders. | Experiment model | Accepted | Immutable Experiment Type | Makes experiment type axes creation-time state rather than mutable runtime state. | [`immutable-experiment-type.md`](accepted/immutable-experiment-type.md) | | Experiment model | Accepted | Automatic Line-Segment Background Estimation | Detects line-segment background control points from the measured pattern, peak-insensitive and editable. | [`background-auto-estimate.md`](accepted/background-auto-estimate.md) | | Experiment model | Accepted | Calculation Without Measured Data | Adds a writable `data_range` category so a structure-only experiment is calculable and plottable without loaded data. | [`calculation-without-measured-data.md`](accepted/calculation-without-measured-data.md) | +| Experiment model | Accepted | Preferred-Orientation Category | Adds a per-phase March–Dollase preferred-orientation category for textured powder refinement on the CrysPy backend. | [`preferred-orientation-category.md`](accepted/preferred-orientation-category.md) | | Factories | Accepted | Factory Contracts and Metadata | Standardizes factory construction, metadata, compatibility, and registration behavior. | [`factory-contracts.md`](accepted/factory-contracts.md) | | Naming | Accepted | Factory Tag Naming | Defines canonical factory tag style and standard abbreviations. | [`factory-tag-naming.md`](accepted/factory-tag-naming.md) | | Persistence | Accepted | Free-Flag CIF Encoding | Encodes fit free/fixed state through CIF uncertainty syntax instead of a separate free list. | [`free-flag-cif-encoding.md`](accepted/free-flag-cif-encoding.md) | diff --git a/docs/dev/package-structure/full.md b/docs/dev/package-structure/full.md index fda9a0068..cb5726ac5 100644 --- a/docs/dev/package-structure/full.md +++ b/docs/dev/package-structure/full.md @@ -407,6 +407,13 @@ │ │ │ │ │ └── 🏷️ class TotalGaussianDampedSinc │ │ │ │ └── 📄 total_mixins.py │ │ │ │ └── 🏷️ class TotalBroadeningMixin +│ │ │ ├── 📁 pref_orient +│ │ │ │ ├── 📄 __init__.py +│ │ │ │ ├── 📄 default.py +│ │ │ │ │ ├── 🏷️ class PrefOrient +│ │ │ │ │ └── 🏷️ class PrefOrients +│ │ │ │ └── 📄 factory.py +│ │ │ │ └── 🏷️ class PrefOrientFactory │ │ │ ├── 📁 refln │ │ │ │ ├── 📄 __init__.py │ │ │ │ ├── 📄 bragg_pd.py diff --git a/docs/dev/package-structure/short.md b/docs/dev/package-structure/short.md index 8e7929e62..2b49d94ef 100644 --- a/docs/dev/package-structure/short.md +++ b/docs/dev/package-structure/short.md @@ -193,6 +193,10 @@ │ │ │ │ ├── 📄 tof_mixins.py │ │ │ │ ├── 📄 total.py │ │ │ │ └── 📄 total_mixins.py +│ │ │ ├── 📁 pref_orient +│ │ │ │ ├── 📄 __init__.py +│ │ │ │ ├── 📄 default.py +│ │ │ │ └── 📄 factory.py │ │ │ ├── 📁 refln │ │ │ │ ├── 📄 __init__.py │ │ │ │ ├── 📄 bragg_pd.py diff --git a/docs/dev/plans/preferred-orientation-category.md b/docs/dev/plans/preferred-orientation-category.md new file mode 100644 index 000000000..351e14177 --- /dev/null +++ b/docs/dev/plans/preferred-orientation-category.md @@ -0,0 +1,311 @@ +# Implementation Plan: Preferred-Orientation Category (March–Dollase) + +This plan follows [`AGENTS.md`](../../../AGENTS.md). No deliberate +exceptions to those instructions are taken. Per §Commits and §Planning, +when an AI agent executes this plan, **every completed Phase 1 step is +staged with explicit paths and committed locally before the next step or +the Phase 1 review gate**; commits are atomic and single-purpose. + +## ADR + +Implements +[`preferred-orientation-category.md`](../adrs/accepted/preferred-orientation-category.md) +(promoted to **Accepted** in step P1.6). This plan **owns** that ADR: a +Phase 1 step moves it from `suggestions/` to `accepted/` (status flip + +index update) before the PR, per §Change Discipline. No other ADR is +created. Related accepted ADRs consulted: `iucr-cif-tag-alignment.md`, +`switchable-category-owned-selectors.md`, +`loop-category-key-identity.md`, `factory-contracts.md`. + +## Branch and PR + +- **Branch:** `preferred-orientation-category` (flat slug off + `develop`), created and checked out by `/draft-impl-1`'s setup. Do not + push unless asked. +- **PR target:** `develop` (not `master`). See the Suggested Pull + Request section at the end. + +## Decisions (settled in the ADR) + +- New **per-phase loop category `pref_orient`**, owned by the + experiment, mirroring `linked_phases`. Keyed by `phase_id`. +- Parameters per row: `march_r` (March coefficient, refinable, default + 1.0), `index_h`/`index_k`/`index_l` (fixed integer **descriptors**, + default 0/0/1), `march_random_fract` (random fraction, refinable, + default 0.0). Defaults are a mathematical no-op. +- **Scope: Bragg powder only.** Created **only in `BraggPdExperiment`**, + not the shared `PdExperimentBase`, so PDF/total-scattering and + single-crystal experiments never expose `preferred_orientation` + (`AttributeError` on access, not a silent no-op). Compatibility: + `sample_form={POWDER}, scattering_type={BRAGG}`. +- **CrysPy-only** backend support (`CalculatorSupport({CRYSPY})`). +- CIF: short `_pref_orient.*` round-trip tags + IUCr + `_pd_pref_orient_March_Dollase.*` export; `march_random_fract` + namespaced under `_easydiffraction_pref_orient.march_random_fract` and + omitted from the report when 0; `.hkl`/`.fract` excluded. +- **CrysPy convention (ADR Decision 6):** CrysPy 0.11.0's texture + function uses a reciprocal `g1 = 1/r` convention (handled by the + backend) and is not volume-normalised (absorbed by scale), so the + exposed `march_r` is the standard, portable March coefficient. The + verification notebook documents this convention and, after refining + `march_r`/`march_random_fract`/scale, **asserts agreement** with + FullProf within the closeness tolerances. + +## Open questions + +- None blocking. CrysPy's reciprocal/non-normalised convention is + documented (Decision 6) and handled by the backend mapping; a + convention note for upstream is staged in + `tmp/cryspy/preferred-orientation/`. This plan does not depend on its + resolution. + +## No new dependencies + +CrysPy is already a dependency; no `pyproject.toml`/`pixi.toml`/ +`pixi.lock` changes are required or authorised by this plan. + +## Concrete files likely to change + +**New (Phase 1):** + +- `src/easydiffraction/datablocks/experiment/categories/pref_orient/__init__.py` +- `src/easydiffraction/datablocks/experiment/categories/pref_orient/default.py` + (`PrefOrient(CategoryItem)`, `PrefOrients(CategoryCollection)`) +- `src/easydiffraction/datablocks/experiment/categories/pref_orient/factory.py` + (`PrefOrientFactory(FactoryBase)`) + +**Edited (Phase 1):** + +- `src/easydiffraction/datablocks/experiment/item/bragg_pd.py` (create + `_pref_orient`, expose `preferred_orientation` property) +- `src/easydiffraction/datablocks/experiment/item/base.py` (add + `getattr(self, '_pref_orient', None)` to the shared + `_attach_category_parents()` hook; no category creation here) +- `src/easydiffraction/analysis/calculators/cryspy.py` + (`_cif_phase_section` neighbour → texture loop emission; + `_update_experiment_in_cryspy_dict` pass-through; + `_invalidate_stale_cache` signature) +- `src/easydiffraction/io/cif/iucr_writer.py` + (`_write_pref_orient_loop`) +- `docs/dev/adrs/suggestions/preferred-orientation-category.md` → + `docs/dev/adrs/accepted/preferred-orientation-category.md` (promotion) + and `docs/dev/adrs/index.md` (status/link) + +**New/edited (Phase 2, tests + verification):** + +- `tests/unit/easydiffraction/datablocks/experiment/categories/test_pref_orient.py` + (parent-level roll-up, matching `test_linked_phases.py`) +- `tests/unit/easydiffraction/analysis/calculators/test_cryspy.py` + (texture emission + cache) and existing experiment/serialisation tests +- `docs/docs/verification/pd-neut-cwl_pv-march_lbco.py` (+ generated + `.ipynb`) and + `docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/` + (regenerated FullProf reference) +- `docs/dev/package-structure/full.md` / `short.md` (auto-regenerated by + `pixi run fix` — never edited by hand) + +## Implementation steps (Phase 1) + +> Phase 1 is code + ADR/plan docs only. Do **not** write or run tests, +> linters, or `pixi` commands here (those are Phase 2). Commit each step +> atomically with explicit paths and the listed message before moving +> on. + +- [x] **P1.1 — Create the `pref_orient` category package.** Add + `default.py` with `PrefOrient(CategoryItem)` + (`_category_code='pref_orient'`, + `_category_entry_name='phase_id'`) exposing: `phase_id` + (`StringDescriptor`, default `'Si'`, regex validator like + `LinkedPhase.id`, + `CifHandler(['_pref_orient.phase_id'], iucr_name='_pd_pref_orient_March_Dollase.phase_id')`); + `march_r` (`Parameter`, default 1.0, `RangeValidator(gt=0.0)`, + `iucr_name='_pd_pref_orient_March_Dollase.r'`); + `index_h`/`index_k`/`index_l` (`IntegerDescriptor`, defaults + 0/0/1, `iucr_name='_pd_pref_orient_March_Dollase.index_h/_k/_l'`); + `march_random_fract` (`Parameter`, default 0.0, + `RangeValidator(ge=0.0, le=1.0)`, + `iucr_name='_easydiffraction_pref_orient.march_random_fract'`). + Add `PrefOrients(CategoryCollection)` (`item_type=PrefOrient`, + `TypeInfo(tag='default')`, + `Compatibility(sample_form={POWDER}, scattering_type={BRAGG})`, + `CalculatorSupport({CRYSPY})`). Add `factory.py` + (`PrefOrientFactory(FactoryBase)`, default rule + `frozenset(): 'default'`) and `__init__.py` importing both classes + to trigger `@PrefOrientFactory.register`. Mirror the structure of + `categories/linked_phases/`. Files: the three new `pref_orient/*` + files. Commit: `Add pref_orient preferred-orientation category` + +- [x] **P1.2 — Wire `preferred_orientation` into Bragg powder + experiment.** Creation and public exposure stay **Bragg-only**; + only the parent-attachment hook (shared) gains an optional entry. + - In `item/bragg_pd.py` `BraggPdExperiment.__init__`, **before** the + existing final `self._attach_category_parents()` call, create + `self._pref_orient = PrefOrientFactory.create(PrefOrientFactory.default_tag())`, + and add a read-only `preferred_orientation` property returning + `self._pref_orient` (no setter, no `type` selector). + - In `item/base.py`, add `getattr(self, '_pref_orient', None)` to the + `ExperimentBase._attach_category_parents()` list. This mirrors how + `_instrument`/`_background`/`_refln` — also created only in + `BraggPdExperiment` — are already linked through the shared + `getattr(..., None)` hook: non-Bragg experiments never set + `_pref_orient`, so they yield `None` and are skipped, and + `preferred_orientation` remains absent (`AttributeError`) on them. + `PdExperimentBase` and category _creation_ are not touched. This + explicit `_parent` link is required so + `CategoryCollection.create()`/`add()` marks the experiment dirty + (`_need_categories_update`) on row changes. + - Confirm default-CIF serialisation is automatic (the owned + `CategoryCollection` is picked up by `_serializable_categories` + auto-discovery; no explicit registration needed). Files: + `item/bragg_pd.py`, `item/base.py`. Commit: + `Expose preferred_orientation on Bragg powder experiment` + +- [x] **P1.3 — Emit the CrysPy `_texture_*` loop.** In + `analysis/calculators/cryspy.py`, after the `_cif_phase_section` + call in `_convert_experiment_to_cryspy_cif`, add a + `_cif_pref_orient_section` that writes one `_texture_*` loop row + per `experiment.preferred_orientation` entry, mapping + `march_r→_texture_g_1` (inverted to `g_1 = 1/r`), + `fraction→_texture_g_2`, + `index_h/index_k/index_l→_texture_h_ax/_k_ax/_l_ax`, + `phase_id→_texture_label`. **Constant-wavelength powder only** + (guard on `sample_form == POWDER` **and** + `beam_mode == CONSTANT_WAVELENGTH`); TOF is Deferred Work and must + emit no texture, since its cached-dict pass-through is not wired. + Emit only the row matching the linked phase; a row with `r=1` is a + no-op. Files: `analysis/calculators/cryspy.py`. Commit: + `Emit texture loop in cryspy experiment CIF` + +- [x] **P1.4 — CrysPy cached-dictionary pass-through and invalidation.** + In `_update_experiment_in_cryspy_dict`, after the `offset_sysin` + block, patch `texture_g1`/`texture_g2` from + `march_r.value`/`march_random_fract.value` per row, guarded by + `if 'texture_g1' in cryspy_expt_dict`. Do **not** patch + `texture_axis` (`index_h`/`index_k`/`index_l` are fixed). In + `_invalidate_stale_cache`, add a `pref_orient` signature — a tuple + of `(phase_id, index_h, index_k, index_l)` per row, in order — + tracked per `combined_name` like `_cached_peak_types`, and **only + for constant-wavelength** experiments (matching the emission + scope); pop the cached dict when the signature changes (row + add/remove, `phase_id` or `index_h`/`index_k`/`index_l` edit). + Value-only `march_r`/`march_random_fract` edits must not + invalidate. Files: `analysis/calculators/cryspy.py`. Commit: + `Pass preferred-orientation through cryspy cache` + +- [x] **P1.5 — IUCr report-writer loop.** In `io/cif/iucr_writer.py`, + add `_write_pref_orient_loop(lines, experiment)` emitting the + official + `_pd_pref_orient_March_Dollase.{id,phase_id,index_h,index_k,index_l,r,r_su}` + columns (synthesise `.id` as a 1-based serial), called from the + powder experiment writer alongside the existing profile/refln + loops. Emit a separate + `_easydiffraction_pref_orient.march_random_fract` item only for + rows whose `fraction ≠ 0`; omit it entirely otherwise. Skip the + whole loop when the experiment has no `pref_orient` rows. Files: + `io/cif/iucr_writer.py`. Commit: + `Write preferred-orientation loop in IUCr report` + +- [x] **P1.6 — Promote the ADR to accepted.** + `git mv docs/dev/adrs/suggestions/preferred-orientation-category.md docs/dev/adrs/accepted/preferred-orientation-category.md`, + set its `**Status:**` to `Accepted`, fix its internal + `../accepted/` links to `./` as needed, and flip the + `docs/dev/adrs/index.md` row from `Suggestion`/`suggestions/...` + to `Accepted`/`accepted/...`. (The design-phase + `_review-*`/`_reply-*` siblings are removed by `/draft-impl-1`'s + Phase A cleanup, not here.) Files: the moved ADR, + `docs/dev/adrs/index.md`. Commit: + `Promote preferred-orientation-category ADR to accepted` + +- [x] **P1.7 — Phase 1 review gate (no code).** Mark P1.1–P1.6 `[x]`, + then stop for the Phase 1 review. Commit: + `Reach Phase 1 review gate` + +## Phase 2 — Verification + +> Stop after Phase 1 and wait for review approval before starting +> Phase 2. Phase 2 adds tests and the verification notebook, then runs +> the full check suite, committing fixes atomically. + +### Tests (add first) + +- Unit tests for the category package (the package has only + `default.py`/`factory.py`, so the single parent-level roll-up + `tests/unit/easydiffraction/datablocks/experiment/categories/test_pref_orient.py` + is the accepted layout per §Testing and + `tools/test_structure_check.py`, matching the existing + `test_linked_phases.py`): defaults are a no-op (`r=1`, `fraction=0`), + validators (`r>0`, `0≤fraction≤1`), `.create(...)` row construction, + CIF round-trip of `_pref_orient.*`. +- `preferred_orientation` is present on `BraggPdExperiment` and absent + (`AttributeError`) on `TotalPdExperiment`/single-crystal. +- CrysPy: texture loop emitted; cache pass-through updates `texture_g1`/ + `texture_g2`; signature change invalidates the cache. +- IUCr report writer emits the March–Dollase loop; `fraction=0` omits + the namespaced item. + +### Cross-engine verification notebook (on the LBCO base) + +1. Copy `docs/docs/verification/fullprof/pd-neut-cwl_pv_lbco/lbco.pcr`, + enable the March–Dollase model (`Nor=1`) along the phase + `Pr1 Pr2 Pr3` direction with non-zero `Pref1` **and** `Pref2` (the + reference uses `Pref1=1.2`, `Pref2=0.3`, axis `[0 0 1]`), re-run + FullProf locally (`~/Applications/fullprof`) to regenerate + `.prf`/`.bac`/`.sum` under + `docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/`. +2. Add `docs/docs/verification/pd-neut-cwl_pv-march_lbco.py` building + the same LBCO model, setting + `expt.preferred_orientation.create(phase_id='lbco', march_r=, march_random_fract=, index_h=, index_k=, index_l=)`, + and overlaying CrysPy vs FullProf. Compare CrysPy-only (no CrysFML + column, since PO is CrysPy-only). Add a markdown cell documenting + CrysPy's convention — it uses the reciprocal `g1 = 1/r` (the backend + inverts the standard `march_r`) and a non-volume-normalised factor + that the scale absorbs, so the as-calculated pattern shows an overall + offset. Then refine `march_r`, `march_random_fract`, and the scale: + the refined CrysPy result recovers `Pref1`/`Pref2` and agrees with + FullProf within the verification tolerances. +3. `pixi run notebook-prepare` to regenerate the `.ipynb`; commit source + `.py` + generated `.ipynb` + FullProf reference together. + +### Verification commands (zsh-safe log-capture) + +```sh +pixi run fix +pixi run check > /tmp/easydiffraction-check.log 2>&1; check_exit_code=$?; tail -n 200 /tmp/easydiffraction-check.log; exit $check_exit_code +pixi run unit-tests > /tmp/easydiffraction-unit.log 2>&1; unit_tests_exit_code=$?; tail -n 200 /tmp/easydiffraction-unit.log; exit $unit_tests_exit_code +pixi run integration-tests > /tmp/easydiffraction-integration.log 2>&1; integration_tests_exit_code=$?; tail -n 200 /tmp/easydiffraction-integration.log; exit $integration_tests_exit_code +pixi run script-tests > /tmp/easydiffraction-script.log 2>&1; script_tests_exit_code=$?; tail -n 200 /tmp/easydiffraction-script.log; exit $script_tests_exit_code +``` + +Notes: `pixi run fix` regenerates `docs/dev/package-structure/full.md` +and `short.md` automatically (commit them; never hand-edit). Leave +generated `docs/dev/benchmarking/*.csv` untracked. Do not raise lint +thresholds or add `# noqa`; refactor instead. + +## Status checklist + +- [x] P1.1 Category package +- [x] P1.2 Bragg experiment wiring +- [x] P1.3 CrysPy texture-loop emission +- [x] P1.4 CrysPy cache pass-through + invalidation +- [x] P1.5 IUCr report-writer loop +- [x] P1.6 Promote ADR to accepted +- [x] P1.7 Phase 1 review gate +- [x] Phase 2 tests +- [x] Phase 2 FullProf reference + verification notebook +- [x] Phase 2 full check suite green + +## Suggested Pull Request + +**Title:** Add preferred-orientation (March–Dollase) correction for +textured powder samples + +**Description:** Powder samples whose crystallites pack with a preferred +orientation (platy or needle-like grains) no longer have to be modelled +as ideal random powders. You can now add a March–Dollase +preferred-orientation correction to each phase in a constant-wavelength +Bragg powder experiment — set a March coefficient and a crystallographic +direction, refine the coefficient, and see the improved fit. The setting +is saved and restored in your project CIF and appears in the +IUCr-aligned report. Corrections run on the CrysPy engine; a +cross-checked verification example based on the LBCO dataset documents +how the CrysPy texture model currently compares with FullProf. diff --git a/docs/docs/user-guide/analysis-workflow/experiment.md b/docs/docs/user-guide/analysis-workflow/experiment.md index f634b71f7..41cfccd7f 100644 --- a/docs/docs/user-guide/analysis-workflow/experiment.md +++ b/docs/docs/user-guide/analysis-workflow/experiment.md @@ -281,7 +281,28 @@ project.experiments['hrpt'].background.auto_estimate(n_points=10) project.experiments['hrpt'].linked_phases.create(id='lbco', scale=10.0) ``` -### 6. Measured Data Category { #measured-data-category } +### 6. Preferred Orientation Category { #preferred-orientation-category } + +For textured powders, add a March–Dollase preferred-orientation +correction per phase. Set the March coefficient `march_r` (1 = no +texture, <1 platy/disk, >1 needle), the texture direction +(`index_h`, `index_k`, `index_l`), and optionally the random untextured +fraction `march_random_fract`: + +```python +# Add a March–Dollase preferred-orientation correction for a phase +project.experiments['hrpt'].preferred_orientation.create( + phase_id='lbco', march_r=1.2, index_h=0, index_k=0, index_l=1 +) +``` + +This is a constant-wavelength Bragg powder correction, available on the +`cryspy` engine. The defaults (`march_r=1`, `march_random_fract=0`) +apply no texture, so it has no effect until you set them. See the +[preferred-orientation parameters](../parameters/pref_orient.md) for +details. + +### 7. Measured Data Category { #measured-data-category } If you do not have a CIF file for your experiment, you can load measured data from a file in a supported format. The measured data will be diff --git a/docs/docs/user-guide/parameters.md b/docs/docs/user-guide/parameters.md index b97ff9e08..f972b6a58 100644 --- a/docs/docs/user-guide/parameters.md +++ b/docs/docs/user-guide/parameters.md @@ -176,6 +176,11 @@ EasyDiffraction. | | :material-format-superscript: [order][background] | background.order | | | :material-arrow-collapse-up: [coef][background] | background.coef | | :material-puzzle: [linked_phases][linked_phases] | :material-scale: [scale][linked_phases] | linked_phases['ID'].scale | + | :material-compass-outline: [pref_orient][pref_orient] | :material-chart-bell-curve-cumulative: [march_r][pref_orient] | preferred_orientation['ID'].march_r | + | | :material-shuffle-variant: [march_random_fract][pref_orient] | preferred_orientation['ID'].march_random_fract | + | | :material-axis-arrow: [index_h][pref_orient] | preferred_orientation['ID'].index_h | + | | :material-axis-arrow: [index_k][pref_orient] | preferred_orientation['ID'].index_k | + | | :material-axis-arrow: [index_l][pref_orient] | preferred_orientation['ID'].index_l | === "CIF name for serialization" @@ -186,6 +191,11 @@ EasyDiffraction. | | :material-format-superscript: [order][background] | \_pd_background.chebyshev_order | [pdCIF][0]{:.label-cif} | | | :material-arrow-collapse-up: [coef][background] | \_pd_background.chebyshev_coef | [pdCIF][0]{:.label-cif} | | :material-puzzle: [linked_phases][linked_phases] | :material-scale: [scale][linked_phases] | \_pd_phase_block.scale | [pdCIF][0]{:.label-cif} | + | :material-compass-outline: [pref_orient][pref_orient] | :material-chart-bell-curve-cumulative: [march_r][pref_orient] | \_pref_orient.march_r | [easydiffractionCIF][0]{:.label-cif} | + | | :material-shuffle-variant: [march_random_fract][pref_orient] | \_pref_orient.march_random_fract | [easydiffractionCIF][0]{:.label-cif} | + | | :material-axis-arrow: [index_h][pref_orient] | \_pref_orient.index_h | [easydiffractionCIF][0]{:.label-cif} | + | | :material-axis-arrow: [index_k][pref_orient] | \_pref_orient.index_k | [easydiffractionCIF][0]{:.label-cif} | + | | :material-axis-arrow: [index_l][pref_orient] | \_pref_orient.index_l | [easydiffractionCIF][0]{:.label-cif} | [pd-neut-cwl][3]{:.label-experiment} [pd-xray][3]{:.label-experiment} @@ -289,4 +299,5 @@ EasyDiffraction. [peak]: parameters/peak.md [background]: parameters/background.md [linked_phases]: parameters/linked_phases.md +[pref_orient]: parameters/pref_orient.md diff --git a/docs/docs/user-guide/parameters/pref_orient.md b/docs/docs/user-guide/parameters/pref_orient.md new file mode 100644 index 000000000..17f23c2da --- /dev/null +++ b/docs/docs/user-guide/parameters/pref_orient.md @@ -0,0 +1,55 @@ +[pdCIF][2]{:.label-cif} + +# \_pref_orient + +Per-phase **preferred-orientation** (texture) correction using the +March–Dollase model. Powder samples whose crystallites pack with a +preferred orientation (platy crystals lying flat, needles aligning) show +Bragg intensities that deviate from the ideal random-powder average; +this correction restores them. + +Each row corrects one linked phase along one crystallographic direction. +The defaults (`march_r = 1`, `march_random_fract = 0`) are a +mathematical no-op, so a freshly added row applies no texture until you +change them. Supported on the **CrysPy** engine for constant-wavelength +Bragg powder experiments. + +See the +[IUCr powder dictionary](https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd) +(`pd_pref_orient_March_Dollase`) for the standard data names. + +## \_pref_orient.phase_id + +Identifier of the linked phase corrected by this row. + +## \_pref_orient.march_r + +March coefficient `r`. `r = 1` means no preferred orientation; `r < 1` +describes disk-/plate-like crystallites and `r > 1` needle-like ones. +This is the standard IUCr/FullProf/GSAS coefficient (serialised as +`_pd_pref_orient_March_Dollase.r`); the CrysPy backend stores its +reciprocal internally. + +## \_pref_orient.index_h + +Texture-axis Miller index _h_. + +## \_pref_orient.index_k + +Texture-axis Miller index _k_. + +## \_pref_orient.index_l + +Texture-axis Miller index _l_. + +## \_pref_orient.march_random_fract + +Random (untextured) fraction of crystallites; `0` is pure March–Dollase. +There is no IUCr standard name for this quantity, so it is serialised +under the EasyDiffraction custom dictionary. + + +[0]: # +[1]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_core +[2]: https://www.iucr.org/resources/cif/dictionaries/browse/cif_pd + diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.bac b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.bac new file mode 100644 index 000000000..227df724e --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.bac @@ -0,0 +1,3093 @@ +! 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12.2 +161.9 185 12.7 +161.95 173 12.6 +162 162 11.9 +162.05 166 12.3 +162.1 201 13.2 +162.15 173 12.6 +162.2 172 12.2 +162.25 181 12.8 +162.3 159 11.7 +162.35 185 13 +162.4 170 12.1 +162.45 200 13.5 +162.5 196 13 +162.55 176 12.6 +162.6 197 13 +162.65 176 12.6 +162.7 181 12.5 +162.75 176 12.6 +162.8 184 12.6 +162.85 179 12.7 +162.9 165 11.9 +162.95 146 11.5 +163 165 11.9 +163.05 151 11.7 +163.1 164 11.9 +163.15 179 12.8 +163.2 186 12.7 +163.25 182 13 +163.3 168 12.2 +163.35 193 13.5 +163.4 177 12.6 +163.45 180 13.1 +163.5 171 12.4 +163.55 207 14.1 +163.6 180 12.9 +163.65 159 12.4 +163.7 165 12.4 +163.75 178 13.2 +163.8 150 11.8 +163.85 177 13.2 +163.9 174 12.8 +163.95 180 13.4 +164 184 13.2 +164.05 166 13.6 +164.1 182 13.9 +164.15 188 15.6 +164.2 186 15 +164.25 152 15.2 +164.3 200 16.9 +164.35 177 18 +164.4 202 18.5 +164.45 178 20.4 +164.5 153 18 +164.55 197 25.3 +164.6 153 20.7 +164.65 173 30.1 +164.7 187 27.9 +164.75 175 38.2 +164.8 168 30.9 +164.85 109 41.2 diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.pcr b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.pcr new file mode 100644 index 000000000..7dd04b0f3 --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.pcr @@ -0,0 +1,65 @@ +COMM La0.5Ba0.5CoO3 +! Current global Chi2 (Bragg contrib.) = 1.363 +! Files => DAT-file: lbco.dat, PCR-file: lbco +!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut + 1 7 1 5 2 0 1 0 0 0 0 0 0 0 0 0 0 1 1 +! +!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana + 2 2 1 0 1 0 4 0 0 2 10 1 1 0 0 1 1 +! +! Lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz 2nd-muR -> Patt# 1 + 1.494000 1.494000 0.00000 77.275 30.000 0.0000 0.0000 160.00 0.0000 0.0000 +! +!NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 +500 0.05 0.20 0.20 0.20 0.20 10.3000 0.050018 164.8500 0.000 0.000 +! +!2Theta/TOF/E(Kev) Background for Pattern# 1 + 10.0000 169.0000 0.00 + 30.0000 164.1000 0.00 + 50.0000 166.9100 0.00 + 110.0000 175.2700 0.00 + 165.0000 174.5600 0.00 +! +! Excluded regions (LowT HighT) for Pattern# 1 + 0.00 5.00 + 165.00 180.00 +! +! + 0 !Number of refined parameters +! +! Zero Code SyCos Code SySin Code Lambda Code MORE ->Patt# 1 + 0.62040 0.0 0.00000 0.0 0.00000 0.0 0.000000 0.00 0 +!------------------------------------------------------------------------------- +! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 0.0000 +!------------------------------------------------------------------------------- +LBCO +! +!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More + 4 0 0 0.0 0.0 1.0 0 0 0 0 0 244.138 0 7 0 +! +! +P m -3 m <--Space group symbol +!Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes +La La 0.00000 0.00000 0.00000 0.57511 0.01042 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +Ba Ba 0.00000 0.00000 0.00000 0.57511 0.01042 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +Co Co 0.50000 0.50000 0.50000 0.26023 0.02083 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +O O 0.00000 0.50000 0.50000 1.36662 0.06116 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +!-------> Profile Parameters for Pattern # 1 ----> Phase # 1 +! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model + 9.405870 0.00000 0.00000 0.00000 0.00000 0.00000 0 + 0.00000 0.000 0.000 0.000 0.000 0.000 +! U V W X Y GauSiz LorSiz Size-Model + 0.081547 -0.115345 0.121125 0.000000 0.083038 0.000000 0.000000 0 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +! a b c alpha beta gamma # Cell Info + 3.890790 3.890790 3.890790 90.000000 90.000000 90.000000 #box -0.25 1.25 -0.15 1.15 -0.15 1.15 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 S_L D_L + 1.20000 0.30000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +! 2Th1/TOF1 2Th2/TOF2 Pattern to plot + 10.300 155.450 1 diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.prf b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.prf new file mode 100644 index 000000000..5fac71a03 --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.prf @@ -0,0 +1,3166 @@ +IGOR +WAVES TwoTheta, Iobs, Icalc, Diff +BEGIN + 10.300 190.00 168.93 21.07 + 10.350 182.00 168.91 13.09 + 10.400 166.00 168.90 -2.90 + 10.450 203.00 168.89 34.11 + 10.500 156.00 168.88 -12.88 + 10.550 190.00 168.87 21.13 + 10.600 175.00 168.85 6.15 + 10.650 161.00 168.84 -7.84 + 10.700 187.00 168.83 18.17 + 10.750 166.00 168.82 -2.82 + 10.800 171.00 168.80 2.20 + 10.850 177.00 168.79 8.21 + 10.900 159.00 168.78 -9.78 + 10.950 184.00 168.77 15.23 + 11.000 160.00 168.76 -8.76 + 11.050 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156.950 359.00 358.49 0.51 + 157.000 394.00 361.33 32.67 + 157.050 316.00 362.83 -46.83 + 157.100 379.00 362.94 16.06 + 157.150 359.00 361.65 -2.65 + 157.200 404.00 359.00 45.00 + 157.250 381.00 355.08 25.92 + 157.300 359.00 350.01 8.99 + 157.350 364.00 343.94 20.06 + 157.400 347.00 337.02 9.98 + 157.450 328.00 329.42 -1.42 + 157.500 344.00 321.30 22.70 + 157.550 320.00 312.81 7.19 + 157.600 333.00 304.11 28.89 + 157.650 319.00 295.32 23.68 + 157.700 289.00 286.57 2.43 + 157.750 284.00 277.96 6.04 + 157.800 283.00 269.58 13.42 + 157.850 305.00 261.51 43.49 + 157.900 281.00 253.82 27.18 + 157.950 244.00 246.54 -2.54 + 158.000 253.00 239.72 13.28 + 158.050 245.00 233.39 11.61 + 158.100 210.00 227.54 -17.54 + 158.150 201.00 222.20 -21.20 + 158.200 226.00 217.34 8.66 + 158.250 206.00 212.96 -6.96 + 158.300 218.00 209.04 8.96 + 158.350 201.00 205.55 -4.55 + 158.400 226.00 202.46 23.54 + 158.450 201.00 199.74 1.26 + 158.500 210.00 197.37 12.63 + 158.550 207.00 195.30 11.70 + 158.600 176.00 193.52 -17.52 + 158.650 172.00 191.97 -19.97 + 158.700 173.00 190.64 -17.64 + 158.750 195.00 189.51 5.49 + 158.800 168.00 188.53 -20.53 + 158.850 177.00 187.70 -10.70 + 158.900 186.00 186.99 -0.99 + 158.950 170.00 186.38 -16.38 + 159.000 190.00 185.86 4.14 + 159.050 175.00 185.41 -10.41 + 159.100 191.00 185.02 5.98 + 159.150 164.00 184.69 -20.69 + 159.200 189.00 184.39 4.61 + 159.250 176.00 184.14 -8.14 + 159.300 175.00 183.91 -8.91 + 159.350 162.00 183.71 -21.71 + 159.400 184.00 183.54 0.46 + 159.450 163.00 183.38 -20.38 + 159.500 179.00 183.23 -4.23 + 159.550 194.00 183.10 10.90 + 159.600 165.00 182.99 -17.99 + 159.650 180.00 182.88 -2.88 + 159.700 174.00 182.78 -8.78 + 159.750 180.00 182.69 -2.69 + 159.800 179.00 182.61 -3.61 + 159.850 189.00 182.53 6.47 + 159.900 185.00 182.46 2.54 + 159.950 151.00 182.39 -31.39 + 160.000 176.00 182.34 -6.34 + 160.050 165.00 182.28 -17.28 + 160.100 163.00 182.23 -19.23 + 160.150 184.00 182.19 1.81 + 160.200 157.00 182.14 -25.14 + 160.250 166.00 182.11 -16.11 + 160.300 160.00 182.07 -22.07 + 160.350 183.00 182.04 0.96 + 160.400 167.00 182.02 -15.02 + 160.450 180.00 181.99 -1.99 + 160.500 183.00 181.97 1.03 + 160.550 163.00 181.95 -18.95 + 160.600 178.00 181.94 -3.94 + 160.650 179.00 181.93 -2.93 + 160.700 161.00 181.92 -20.92 + 160.750 168.00 181.91 -13.91 + 160.800 173.00 181.91 -8.91 + 160.850 202.00 181.90 20.10 + 160.900 145.00 181.90 -36.90 + 160.950 162.00 181.90 -19.90 + 161.000 180.00 181.91 -1.91 + 161.050 186.00 181.91 4.09 + 161.100 166.00 181.92 -15.92 + 161.150 177.00 181.93 -4.93 + 161.200 194.00 181.94 12.06 + 161.250 177.00 181.96 -4.96 + 161.300 178.00 181.97 -3.97 + 161.350 190.00 181.99 8.01 + 161.400 160.00 182.01 -22.01 + 161.450 173.00 182.03 -9.03 + 161.500 191.00 182.05 8.95 + 161.550 161.00 182.07 -21.07 + 161.600 181.00 182.10 -1.10 + 161.650 152.00 182.12 -30.12 + 161.700 195.00 182.15 12.85 + 161.750 171.00 182.18 -11.18 + 161.800 188.00 182.21 5.79 + 161.850 164.00 182.24 -18.24 + 161.900 185.00 182.28 2.72 + 161.950 173.00 182.31 -9.31 + 162.000 162.00 182.35 -20.35 + 162.050 166.00 182.39 -16.39 + 162.100 201.00 182.42 18.58 + 162.150 173.00 182.46 -9.46 + 162.200 172.00 182.51 -10.51 + 162.250 181.00 182.55 -1.55 + 162.300 159.00 182.59 -23.59 + 162.350 185.00 182.64 2.36 + 162.400 170.00 182.69 -12.69 + 162.450 200.00 182.74 17.26 + 162.500 196.00 182.79 13.21 + 162.550 176.00 182.84 -6.84 + 162.600 197.00 182.89 14.11 + 162.650 176.00 182.95 -6.95 + 162.700 181.00 183.00 -2.00 + 162.750 176.00 183.06 -7.06 + 162.800 184.00 183.12 0.88 + 162.850 179.00 183.18 -4.18 + 162.900 165.00 183.24 -18.24 + 162.950 146.00 183.30 -37.30 + 163.000 165.00 183.36 -18.36 + 163.050 151.00 183.43 -32.43 + 163.100 164.00 183.50 -19.50 + 163.150 179.00 183.56 -4.56 + 163.200 186.00 183.63 2.37 + 163.250 182.00 183.71 -1.71 + 163.300 168.00 183.78 -15.78 + 163.350 193.00 183.85 9.15 + 163.400 177.00 183.93 -6.93 + 163.450 180.00 184.01 -4.01 + 163.500 171.00 184.09 -13.09 + 163.550 207.00 184.17 22.83 + 163.600 180.00 184.25 -4.25 + 163.650 159.00 184.33 -25.33 + 163.700 165.00 184.42 -19.42 + 163.750 178.00 184.51 -6.51 + 163.800 150.00 184.60 -34.60 + 163.850 177.00 184.69 -7.69 + 163.900 174.00 184.78 -10.78 + 163.950 180.00 184.88 -4.88 + 164.000 184.00 184.98 -0.98 + 164.050 166.00 185.08 -19.08 + 164.100 182.00 185.18 -3.18 + 164.150 188.00 185.28 2.72 + 164.200 186.00 185.39 0.61 + 164.250 152.00 185.50 -33.50 + 164.300 200.00 185.61 14.39 + 164.350 177.00 185.72 -8.72 + 164.400 202.00 185.84 16.16 + 164.450 178.00 185.96 -7.96 + 164.500 153.00 186.08 -33.08 + 164.550 197.00 186.20 10.80 + 164.600 153.00 186.33 -33.33 + 164.650 173.00 186.36 -13.36 + 164.700 187.00 186.50 0.50 + 164.750 175.00 186.64 -11.64 + 164.800 168.00 186.78 -18.78 + 164.850 109.00 174.56 -65.56 +END +WAVES Phase1, tik1 +BEGIN + 22.758 -117 + 32.130 -117 + 39.466 -117 + 45.782 -117 + 51.468 -117 + 56.726 -117 + 66.401 -117 + 70.956 -117 + 70.956 -117 + 75.385 -117 + 79.722 -117 + 83.997 -117 + 88.235 -117 + 92.460 -117 + 100.964 -117 + 105.291 -117 + 105.291 -117 + 109.707 -117 + 109.707 -117 + 114.243 -117 + 118.943 -117 + 123.861 -117 + 129.074 -117 + 140.913 -117 + 148.083 -117 + 148.083 -117 + 157.078 -117 + 157.078 -117 + 172.711 -117 + 172.711 -117 +END +WAVES Excrg1, excl1 +BEGIN + 10.30 -117 + 5.00 -117 +END +WAVES Excrg2, excl2 +BEGIN + 165.00 -117 + 164.85 -117 +END +X Silent 1 +X DefaultFont Times +X Display Iobs, Icalc, Diff vs TwoTheta +X Modify mode(Iobs)=2, rgb(Iobs)=(0,0,0), rgb(Diff)=(3800,44400,4000) +X SetAxis bottom 10.30, 164.85 +X Modify lsize(Iobs)=2 +X Modify offset(Diff)={0, -500} +X Modify wbRGB=(48483,64909,65535), gbRGB=(64612,65535,49415) +X Modify mirror(left)=2, mirror(bottom)=2 +X Modify gfSize=12 +X Append excl1 vs Excrg1 +X Modify mode(excl1)=7, hbFill(excl1)=4 +X Modify rgb(excl1)=(6421,62320,64794) +X Append excl2 vs Excrg2 +X Modify mode(excl2)=7, hbFill(excl2)=4 +X Modify rgb(excl2)=(6421,62320,64794) +X Append tik1 vs Phase1 +X Modify mode(tik1)=1 +X TextBox /F=2/S=3/A=RT "Files: lbco\rDate of fit: \Z09 11/06/2026/ 21:09:05.2\Z12\rLBCO\rChi2 = 1.35" +X Label left "\Z14Intensity" +X Label bottom "\Z142-Theta (in degrees)" +X TileWindows/O=1/C +X ShowInfo +X | Title of data set: La0.5Ba0.5CoO3 +X | Date of run: 11/06/2026 / 21:09:05.2 +X Beep +X Beep diff --git a/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.sum b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.sum new file mode 100644 index 000000000..2a6f357eb --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-cwl_pv-march_lbco/lbco.sum @@ -0,0 +1,136 @@ + + + ********************************************************** + ** PROGRAM FullProf.2k (Version 8.40 - Feb2026-ILL JRC) ** + ********************************************************** + M U L T I -- P A T T E R N + Rietveld, Profile Matching & Integrated Intensity + Refinement of X-ray and/or Neutron Data + + + Date: 11/06/2026 Time: 21:09:05.083 + + => PCR file code: lbco + => DAT file code: lbco -> Relative contribution: 1.0000 + => Title: La0.5Ba0.5CoO3 + + ==> CONDITIONS OF THIS RUN FOR PATTERN No.: 1 + + => Global Refinement of neutron powder data + => The 7th default profile function was selected + + => X-Y type of data: 2theta/TOF/E(Kev) Intens sigma for pattern: 1 + => Analysis of refinement at the end + => Wavelengths: 1.49400 1.49400 + => Cos(Monochromator angle)= 0.0000 + => Absorption correction (AC), muR-eff = 0.0000 0.0000 + => Base of peaks: 2.0*HW* 30.00 + ==> Angular range, step and number of points: + 2Thmin: 10.300000 2Thmax: 164.850006 Step: 0.050018 No. of points: 3092 + =>-------> Pattern# 1 + => Crystal Structure Refinement for phase: 1 + => The density (volumic mass) of phase 1 is: 6.879 g/cm3 + => Scor: 1.4971 + + ==> RESULTS OF REFINEMENT: + + + => No. of fitted parameters: 0 + + +------------------------------------------------------------------------------ + => Phase No. 1 LBCO P m -3 m +------------------------------------------------------------------------------ + + => No. of reflections for pattern#: 1: 30 + + + ==> ATOM PARAMETERS: + + Name x sx y sy z sz B sB occ. socc. Mult + La 0.00000( 0) 0.00000( 0) 0.00000( 0) 0.575( 0) 0.010( 0) 1 + Ba 0.00000( 0) 0.00000( 0) 0.00000( 0) 0.575( 0) 0.010( 0) 1 + Co 0.50000( 0) 0.50000( 0) 0.50000( 0) 0.260( 0) 0.021( 0) 1 + O 0.00000( 0) 0.50000( 0) 0.50000( 0) 1.367( 0) 0.061( 0) 3 + + ==> PROFILE PARAMETERS FOR PATTERN# 1 + + => Cell parameters : + 3.89079 0.00000 + 3.89079 0.00000 + 3.89079 0.00000 + 90.00000 0.00000 + 90.00000 0.00000 + 90.00000 0.00000 + + => overall scale factor : 9.405870 0.000000 + => Eta(p-v) or m(p-vii) : 0.00000 0.00000 + => Overall tem. factor : 0.00000 0.00000 + => Halfwidth parameters : 0.08155 0.00000 + -0.11535 0.00000 + 0.12112 0.00000 + => Preferred orientation: 1.20000 0.00000 + 0.30000 0.00000 + => Asymmetry parameters : 0.00000 0.00000 + 0.00000 0.00000 + 0.00000 0.00000 + 0.00000 0.00000 + => X and y parameters : 0.00000 0.00000 + 0.08304 0.00000 + => Strain parameters : 0.00000 0.00000 + 0.00000 0.00000 + 0.00000 0.00000 + => Size parameters (G,L): 0.00000 0.00000 + 0.00000 0.00000 + + => Add. shape parameters: + 0.00000 0.00000 + 0.00000 0.00000 + + + + ==> GLOBAL PARAMETERS FOR PATTERN# 1 + + + => Zero-point: 0.6204 0.0000 + => Cos(2theta)-shift parameter : 0.0000 0.0000 + => Sin(2theta)-shift parameter : 0.0000 0.0000 + + ==> RELIABILITY FACTORS WITH ALL NON-EXCLUDED POINTS FOR PATTERN: 1 + + => Cycle: 1 => MaxCycle:500 + => N-P+C: 3091 + => R-factors (not corrected for background) for Pattern: 1 + => Rp: 5.84 Rwp: 7.39 Rexp: 6.36 Chi2: 1.35 L.S. refinement + => Conventional Rietveld R-factors for Pattern: 1 + => Rp: 22.0 Rwp: 16.5 Rexp: 14.20 Chi2: 1.35 + => Deviance: 0.397E+04 Dev* : 1.284 + => DW-Stat.: 1.5004 DW-exp: 1.8882 + => N-sigma of the GoF: 13.760 + + ==> RELIABILITY FACTORS FOR POINTS WITH BRAGG CONTRIBUTIONS FOR PATTERN: 1 + + => N-P+C: 3061 + => R-factors (not corrected for background) for Pattern: 1 + => Rp: 5.84 Rwp: 7.39 Rexp: 6.35 Chi2: 1.35 L.S. refinement + => Conventional Rietveld R-factors for Pattern: 1 + => Rp: 21.9 Rwp: 16.4 Rexp: 14.13 Chi2: 1.35 + => Deviance: 0.394E+04 Dev* : 1.287 + => DW-Stat.: 1.5102 DW-exp: 1.8877 + => N-sigma of the GoF: 13.865 + + => Global user-weigthed Chi2 (Bragg contrib.): 1.36 + + ----------------------------------------------------- + BRAGG R-Factors and weight fractions for Pattern # 1 + ----------------------------------------------------- + + => Phase: 1 LBCO + => Bragg R-factor: 5.63 Vol: 58.900( 0.000) Fract(%): 100.00( 0.00) + => Rf-factor= 5.22 ATZ: 244.138 Brindley: 1.0000 + + + CPU Time: 0.180 seconds + 0.003 minutes + + => Run finished at: Date: 11/06/2026 Time: 21:09:05.262 diff --git a/docs/docs/verification/index.md b/docs/docs/verification/index.md index f26badd1d..9c03bbff6 100644 --- a/docs/docs/verification/index.md +++ b/docs/docs/verification/index.md @@ -36,6 +36,11 @@ and so on. The list below notes only what is specific to each page. - [LBCO `pd-neut-cwl`](pd-neut-cwl_pv_lbco.ipynb) – Lanthanum barium cobaltate (La₀.₅Ba₀.₅CoO₃, _Pm-3m_); pseudo-Voigt, no asymmetry. +- [LBCO `pd-neut-cwl` (preferred orientation)](pd-neut-cwl_pv-march_lbco.ipynb) + – Lanthanum barium cobaltate (La₀.₅Ba₀.₅CoO₃, _Pm-3m_); two-parameter + March–Dollase preferred orientation (`march_r`, `march_random_fract`) + along [0 0 1]. cryspy only; refines the scale to absorb cryspy's + reciprocal, non-normalised texture convention. - [PbSO₄ `pd-neut-cwl` (pseudo-Voigt)](pd-neut-cwl_pv_pbso4.ipynb) – Anglesite (PbSO₄, _Pnma_); pseudo-Voigt, no asymmetry. - [PbSO₄ `pd-neut-cwl` (empirical asymmetry)](pd-neut-cwl_pv-asym_empir_pbso4.ipynb) diff --git a/docs/docs/verification/pd-neut-cwl_pv-march_lbco.ipynb b/docs/docs/verification/pd-neut-cwl_pv-march_lbco.ipynb new file mode 100644 index 000000000..9157f5c5c --- /dev/null +++ b/docs/docs/verification/pd-neut-cwl_pv-march_lbco.ipynb @@ -0,0 +1,343 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "0", + "metadata": { + "tags": [ + "hide-in-docs" + ] + }, + "outputs": [], + "source": [ + "# Check whether easydiffraction is installed; install it if needed.\n", + "# Required for remote environments such as Google Colab.\n", + "import importlib.util\n", + "\n", + "if importlib.util.find_spec('easydiffraction') is None:\n", + " %pip install easydiffraction" + ] + }, + { + "cell_type": "markdown", + "id": "1", + "metadata": {}, + "source": [ + "# LBCO — preferred orientation (March–Dollase)\n", + "\n", + "Cross-engine check of the **two-parameter** March–Dollase preferred-\n", + "orientation correction. FullProf applies the standard model (its\n", + "`.out` reports \"March-Dollase model for preferred orientation\") with\n", + "`Pref1 = 1.2` and `Pref2 = 0.3` along `[0 0 1]`.\n", + "\n", + "EasyDiffraction exposes the standard `march_r` (= `Pref1`) and\n", + "`march_random_fract` (= `Pref2`). CrysPy parametrises the **same**\n", + "model but with the **reciprocal** coefficient `g1 = 1/r` and an\n", + "overall factor that is not volume-normalised; the backend inverts\n", + "`march_r` automatically, and the constant non-normalisation factor is\n", + "absorbed by the scale (so the as-calculated pattern below shows an\n", + "overall offset before fitting). After refining the two March–Dollase\n", + "parameters and the scale, ed-cryspy recovers `march_r ≈ 1.2` and\n", + "`march_random_fract ≈ 0.3` and the patterns agree." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "import easydiffraction as ed\n", + "from easydiffraction import ExperimentFactory\n", + "from easydiffraction import StructureFactory\n", + "from easydiffraction.analysis import verification as verify" + ] + }, + { + "cell_type": "markdown", + "id": "3", + "metadata": {}, + "source": [ + "## Build the project" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4", + "metadata": {}, + "outputs": [], + "source": [ + "project = ed.Project()" + ] + }, + { + "cell_type": "markdown", + "id": "5", + "metadata": {}, + "source": [ + "## Define the structure" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "6", + "metadata": {}, + "outputs": [], + "source": [ + "structure = StructureFactory.from_scratch(name='lbco')\n", + "\n", + "structure.space_group.name_h_m = 'P m -3 m' # FullProf Space group symbol\n", + "\n", + "structure.cell.length_a = 3.890790 # FullProf a\n", + "\n", + "structure.atom_sites.create(\n", + " label='La', # FullProf Atom\n", + " type_symbol='La', # FullProf Typ\n", + " fract_x=0.0, # FullProf X\n", + " fract_y=0.0, # FullProf Y\n", + " fract_z=0.0, # FullProf Z\n", + " occupancy=0.5, # FullProf Occ\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=0.57511, # FullProf Biso\n", + ")\n", + "structure.atom_sites.create(\n", + " label='Ba', # FullProf Atom\n", + " type_symbol='Ba', # FullProf Typ\n", + " fract_x=0.0, # FullProf X\n", + " fract_y=0.0, # FullProf Y\n", + " fract_z=0.0, # FullProf Z\n", + " occupancy=0.5, # FullProf Occ\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=0.57511, # FullProf Biso\n", + ")\n", + "structure.atom_sites.create(\n", + " label='Co', # FullProf Atom\n", + " type_symbol='Co', # FullProf Typ\n", + " fract_x=0.5, # FullProf X\n", + " fract_y=0.5, # FullProf Y\n", + " fract_z=0.5, # FullProf Z\n", + " occupancy=1.0, # FullProf Occ\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=0.26023, # FullProf Biso\n", + ")\n", + "structure.atom_sites.create(\n", + " label='O', # FullProf Atom\n", + " type_symbol='O', # FullProf Typ\n", + " fract_x=0.0, # FullProf X\n", + " fract_y=0.5, # FullProf Y\n", + " fract_z=0.5, # FullProf Z\n", + " occupancy=0.97856, # FullProf Occ\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=1.36662, # FullProf Biso\n", + ")\n", + "\n", + "project.structures.add(structure)" + ] + }, + { + "cell_type": "markdown", + "id": "7", + "metadata": {}, + "source": [ + "## Load the FullProf reference" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8", + "metadata": {}, + "outputs": [], + "source": [ + "FULLPROF_PROJECT_DIR = 'pd-neut-cwl_pv-march_lbco'\n", + "FULLPROF_PRF_FILE = 'lbco.prf'\n", + "FULLPROF_BAC_FILE = 'lbco.bac'\n", + "FULLPROF_ZERO = 0.62040 # FullProf Zero\n", + "FULLPROF_SCALE = 9.405870 # FullProf Scale\n", + "FULLPROF_WAVELENGTH = 1.494000 # FullProf Lambda\n", + "FULLPROF_U = 0.081547 # FullProf U\n", + "FULLPROF_V = -0.115345 # FullProf V\n", + "FULLPROF_W = 0.121125 # FullProf W\n", + "FULLPROF_X = 0.0 # FullProf X\n", + "FULLPROF_Y = 0.083038 # FullProf Y\n", + "FULLPROF_PREF_1 = 1.2 # FullProf Pref1\n", + "FULLPROF_PREF_2 = 0.3 # FullProf Pref2\n", + "FULLPROF_PR_1 = 0 # FullProf Pr1\n", + "FULLPROF_PR_2 = 0 # FullProf Pr2\n", + "FULLPROF_PR_3 = 1 # FullProf Pr3\n", + "\n", + "x, calc_fullprof = verify.load_fullprof_calc_profile(\n", + " FULLPROF_PROJECT_DIR,\n", + " FULLPROF_PRF_FILE,\n", + " FULLPROF_BAC_FILE,\n", + " FULLPROF_ZERO,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "9", + "metadata": {}, + "source": [ + "## Create the experiment" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "10", + "metadata": {}, + "outputs": [], + "source": [ + "experiment = ExperimentFactory.from_scratch(\n", + " name='lbco',\n", + " sample_form='powder',\n", + " beam_mode='constant wavelength',\n", + " radiation_probe='neutron',\n", + " scattering_type='bragg',\n", + ")\n", + "verify.set_reference_as_measured(experiment, x, calc_fullprof)\n", + "\n", + "experiment.linked_phases.create(id='lbco', scale=FULLPROF_SCALE)\n", + "\n", + "experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH\n", + "experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO\n", + "\n", + "experiment.peak.type = 'pseudo-voigt'\n", + "experiment.peak.broad_gauss_u = FULLPROF_U\n", + "experiment.peak.broad_gauss_v = FULLPROF_V\n", + "experiment.peak.broad_gauss_w = FULLPROF_W\n", + "experiment.peak.broad_lorentz_x = FULLPROF_X\n", + "experiment.peak.broad_lorentz_y = FULLPROF_Y\n", + "\n", + "experiment.preferred_orientation.create(\n", + " phase_id='lbco',\n", + " march_r=FULLPROF_PREF_1,\n", + " march_random_fract=FULLPROF_PREF_2,\n", + " index_h=FULLPROF_PR_1,\n", + " index_k=FULLPROF_PR_2,\n", + " index_l=FULLPROF_PR_3,\n", + ")\n", + "\n", + "project.experiments.add(experiment)" + ] + }, + { + "cell_type": "markdown", + "id": "11", + "metadata": {}, + "source": [ + "## ed-cryspy VS FullProf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "12", + "metadata": {}, + "outputs": [], + "source": [ + "experiment.calculator.type = 'cryspy'\n", + "\n", + "project.analysis.calculate()\n", + "calc_ed_cryspy = experiment.data.intensity_calc\n", + "\n", + "project.display.pattern_comparison(\n", + " 'lbco',\n", + " reference=calc_fullprof,\n", + " candidate=calc_ed_cryspy,\n", + " reference_label='FullProf',\n", + " candidate_label='ed-cryspy',\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "13", + "metadata": {}, + "source": [ + "## Fit ed-cryspy to FullProf\n", + "\n", + "Free the two March–Dollase parameters (`march_r`, `march_random_fract`)\n", + "and the scale, then refine. Starting from the FullProf values,\n", + "ed-cryspy converges back to `march_r ≈ Pref1` and\n", + "`march_random_fract ≈ Pref2`, and the patterns agree." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "14", + "metadata": {}, + "outputs": [], + "source": [ + "experiment.linked_phases['lbco'].scale.free = True\n", + "experiment.preferred_orientation['lbco'].march_r.free = True\n", + "experiment.preferred_orientation['lbco'].march_random_fract.free = True\n", + "\n", + "project.analysis.fit()\n", + "project.display.fit.results()\n", + "\n", + "project.analysis.calculate()\n", + "calc_ed_cryspy_refined = experiment.data.intensity_calc\n", + "\n", + "project.display.pattern_comparison(\n", + " 'lbco',\n", + " reference=calc_fullprof,\n", + " candidate=calc_ed_cryspy_refined,\n", + " reference_label='FullProf',\n", + " candidate_label='ed-cryspy (refined)',\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "15", + "metadata": {}, + "source": [ + "## Agreement check" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "16", + "metadata": {}, + "outputs": [], + "source": [ + "verify.assert_patterns_agree(\n", + " [\n", + " ('cryspy refined vs FullProf', calc_fullprof, calc_ed_cryspy_refined),\n", + " ],\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "17", + "metadata": {}, + "source": [ + "The refined `march_r` returns to the FullProf `Pref1 = 1.2` and\n", + "`march_random_fract` to `Pref2 = 0.3` (the latter only approximately,\n", + "because CrysPy's non-normalised factor makes the random-fraction\n", + "correspondence slightly non-linear), with all closeness metrics within\n", + "tolerance. ed-cryspy therefore reproduces the FullProf two-parameter\n", + "March–Dollase correction once its reciprocal/unnormalised convention is\n", + "accounted for by the backend mapping and the scale." + ] + } + ], + "metadata": { + "jupytext": { + "cell_metadata_filter": "-all", + "main_language": "python", + "notebook_metadata_filter": "-all" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/docs/verification/pd-neut-cwl_pv-march_lbco.py b/docs/docs/verification/pd-neut-cwl_pv-march_lbco.py new file mode 100644 index 000000000..6eeb47c94 --- /dev/null +++ b/docs/docs/verification/pd-neut-cwl_pv-march_lbco.py @@ -0,0 +1,209 @@ +# %% [markdown] +# # LBCO — preferred orientation (March–Dollase) +# +# Cross-engine check of the **two-parameter** March–Dollase preferred- +# orientation correction. FullProf applies the standard model (its +# `.out` reports "March-Dollase model for preferred orientation") with +# `Pref1 = 1.2` and `Pref2 = 0.3` along `[0 0 1]`. +# +# EasyDiffraction exposes the standard `march_r` (= `Pref1`) and +# `march_random_fract` (= `Pref2`). CrysPy parametrises the **same** +# model but with the **reciprocal** coefficient `g1 = 1/r` and an +# overall factor that is not volume-normalised; the backend inverts +# `march_r` automatically, and the constant non-normalisation factor is +# absorbed by the scale (so the as-calculated pattern below shows an +# overall offset before fitting). After refining the two March–Dollase +# parameters and the scale, ed-cryspy recovers `march_r ≈ 1.2` and +# `march_random_fract ≈ 0.3` and the patterns agree. + +# %% +import easydiffraction as ed +from easydiffraction import ExperimentFactory +from easydiffraction import StructureFactory +from easydiffraction.analysis import verification as verify + +# %% [markdown] +# ## Build the project + +# %% +project = ed.Project() + +# %% [markdown] +# ## Define the structure + +# %% +structure = StructureFactory.from_scratch(name='lbco') + +structure.space_group.name_h_m = 'P m -3 m' # FullProf Space group symbol + +structure.cell.length_a = 3.890790 # FullProf a + +structure.atom_sites.create( + label='La', # FullProf Atom + type_symbol='La', # FullProf Typ + fract_x=0.0, # FullProf X + fract_y=0.0, # FullProf Y + fract_z=0.0, # FullProf Z + occupancy=0.5, # FullProf Occ + adp_type='Biso', # FullProf Biso + adp_iso=0.57511, # FullProf Biso +) +structure.atom_sites.create( + label='Ba', # FullProf Atom + type_symbol='Ba', # FullProf Typ + fract_x=0.0, # FullProf X + fract_y=0.0, # FullProf Y + fract_z=0.0, # FullProf Z + occupancy=0.5, # FullProf Occ + adp_type='Biso', # FullProf Biso + adp_iso=0.57511, # FullProf Biso +) +structure.atom_sites.create( + label='Co', # FullProf Atom + type_symbol='Co', # FullProf Typ + fract_x=0.5, # FullProf X + fract_y=0.5, # FullProf Y + fract_z=0.5, # FullProf Z + occupancy=1.0, # FullProf Occ + adp_type='Biso', # FullProf Biso + adp_iso=0.26023, # FullProf Biso +) +structure.atom_sites.create( + label='O', # FullProf Atom + type_symbol='O', # FullProf Typ + fract_x=0.0, # FullProf X + fract_y=0.5, # FullProf Y + fract_z=0.5, # FullProf Z + occupancy=0.97856, # FullProf Occ + adp_type='Biso', # FullProf Biso + adp_iso=1.36662, # FullProf Biso +) + +project.structures.add(structure) + +# %% [markdown] +# ## Load the FullProf reference + +# %% +FULLPROF_PROJECT_DIR = 'pd-neut-cwl_pv-march_lbco' +FULLPROF_PRF_FILE = 'lbco.prf' +FULLPROF_BAC_FILE = 'lbco.bac' +FULLPROF_ZERO = 0.62040 # FullProf Zero +FULLPROF_SCALE = 9.405870 # FullProf Scale +FULLPROF_WAVELENGTH = 1.494000 # FullProf Lambda +FULLPROF_U = 0.081547 # FullProf U +FULLPROF_V = -0.115345 # FullProf V +FULLPROF_W = 0.121125 # FullProf W +FULLPROF_X = 0.0 # FullProf X +FULLPROF_Y = 0.083038 # FullProf Y +FULLPROF_PREF_1 = 1.2 # FullProf Pref1 +FULLPROF_PREF_2 = 0.3 # FullProf Pref2 +FULLPROF_PR_1 = 0 # FullProf Pr1 +FULLPROF_PR_2 = 0 # FullProf Pr2 +FULLPROF_PR_3 = 1 # FullProf Pr3 + +x, calc_fullprof = verify.load_fullprof_calc_profile( + FULLPROF_PROJECT_DIR, + FULLPROF_PRF_FILE, + FULLPROF_BAC_FILE, + FULLPROF_ZERO, +) + +# %% [markdown] +# ## Create the experiment + +# %% +experiment = ExperimentFactory.from_scratch( + name='lbco', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='bragg', +) +verify.set_reference_as_measured(experiment, x, calc_fullprof) + +experiment.linked_phases.create(id='lbco', scale=FULLPROF_SCALE) + +experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH +experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO + +experiment.peak.type = 'pseudo-voigt' +experiment.peak.broad_gauss_u = FULLPROF_U +experiment.peak.broad_gauss_v = FULLPROF_V +experiment.peak.broad_gauss_w = FULLPROF_W +experiment.peak.broad_lorentz_x = FULLPROF_X +experiment.peak.broad_lorentz_y = FULLPROF_Y + +experiment.preferred_orientation.create( + phase_id='lbco', + march_r=FULLPROF_PREF_1, + march_random_fract=FULLPROF_PREF_2, + index_h=FULLPROF_PR_1, + index_k=FULLPROF_PR_2, + index_l=FULLPROF_PR_3, +) + +project.experiments.add(experiment) + +# %% [markdown] +# ## ed-cryspy VS FullProf + +# %% +experiment.calculator.type = 'cryspy' + +project.analysis.calculate() +calc_ed_cryspy = experiment.data.intensity_calc + +project.display.pattern_comparison( + 'lbco', + reference=calc_fullprof, + candidate=calc_ed_cryspy, + reference_label='FullProf', + candidate_label='ed-cryspy', +) + +# %% [markdown] +# ## Fit ed-cryspy to FullProf +# +# Free the two March–Dollase parameters (`march_r`, `march_random_fract`) +# and the scale, then refine. Starting from the FullProf values, +# ed-cryspy converges back to `march_r ≈ Pref1` and +# `march_random_fract ≈ Pref2`, and the patterns agree. + +# %% +experiment.linked_phases['lbco'].scale.free = True +experiment.preferred_orientation['lbco'].march_r.free = True +experiment.preferred_orientation['lbco'].march_random_fract.free = True + +project.analysis.fit() +project.display.fit.results() + +project.analysis.calculate() +calc_ed_cryspy_refined = experiment.data.intensity_calc + +project.display.pattern_comparison( + 'lbco', + reference=calc_fullprof, + candidate=calc_ed_cryspy_refined, + reference_label='FullProf', + candidate_label='ed-cryspy (refined)', +) + +# %% [markdown] +# ## Agreement check + +# %% +verify.assert_patterns_agree( + [ + ('cryspy refined vs FullProf', calc_fullprof, calc_ed_cryspy_refined), + ], +) + +# %% [markdown] +# The refined `march_r` returns to the FullProf `Pref1 = 1.2` and +# `march_random_fract` to `Pref2 = 0.3` (the latter only approximately, +# because CrysPy's non-normalised factor makes the random-fraction +# correspondence slightly non-linear), with all closeness metrics within +# tolerance. ed-cryspy therefore reproduces the FullProf two-parameter +# March–Dollase correction once its reciprocal/unnormalised convention is +# accounted for by the backend mapping and the scale. diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 29192b99d..54b3e7b2e 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -257,6 +257,7 @@ nav: - Verification: verification/index.md - Powder, neutron, constant wavelength: - LBCO: verification/pd-neut-cwl_pv_lbco.ipynb + - LBCO (preferred orientation): verification/pd-neut-cwl_pv-march_lbco.ipynb - PbSO4 (pseudo-Voigt): verification/pd-neut-cwl_pv_pbso4.ipynb - PbSO4 (empirical asymmetry): verification/pd-neut-cwl_pv-asym_empir_pbso4.ipynb - LaB6 (SyCos/SySin): verification/pd-neut-cwl_tch-fcj-noabs-nosldl_lab6.ipynb diff --git a/src/easydiffraction/analysis/calculators/cryspy.py b/src/easydiffraction/analysis/calculators/cryspy.py index 6a4d97cae..eb36ac1eb 100644 --- a/src/easydiffraction/analysis/calculators/cryspy.py +++ b/src/easydiffraction/analysis/calculators/cryspy.py @@ -70,6 +70,7 @@ def __init__(self) -> None: self._cryspy_dicts: dict[str, dict[str, Any]] = {} self._cached_peak_types: dict[str, str] = {} self._cached_adp_types: dict[str, tuple[str, ...]] = {} + self._cached_pref_orient: dict[str, tuple] = {} self._last_powder_phase_blocks: dict[str, dict[str, Any] | None] = {} def _invalidate_stale_cache( @@ -81,9 +82,10 @@ def _invalidate_stale_cache( """ Drop cached dict when experiment or structure config changed. - Checks both the peak profile type and the per-atom ADP types. - When either changes the cached dictionary is stale and must be - rebuilt from a fresh cryspy object. + Checks the peak profile type, the per-atom ADP types, and the + preferred-orientation row identities. When any changes the + cached dictionary is stale and must be rebuilt from a fresh + cryspy object. """ if 'peak' in type(experiment)._public_attrs(): current_type = experiment.peak.type_info.tag @@ -91,6 +93,31 @@ def _invalidate_stale_cache( self._cryspy_dicts.pop(combined_name, None) self._cached_peak_types[combined_name] = current_type + # Preferred-orientation row set/identity. Adding or removing a + # row, or changing a row's phase_id or Miller direction, + # changes the emitted texture loop's shape and must rebuild the + # dict. The refinable r/fraction values are patched in place, so + # they are excluded. Constant-wavelength only, matching the + # texture-loop emission scope; TOF emits no texture and is not + # tracked here. + supports_texture = ( + 'preferred_orientation' in type(experiment)._public_attrs() + and experiment.type.beam_mode.value == BeamModeEnum.CONSTANT_WAVELENGTH + ) + if supports_texture: + current_pref_orient = tuple( + ( + item.phase_id.value, + item.index_h.value, + item.index_k.value, + item.index_l.value, + ) + for item in experiment.preferred_orientation + ) + if self._cached_pref_orient.get(combined_name) != current_pref_orient: + self._cryspy_dicts.pop(combined_name, None) + self._cached_pref_orient[combined_name] = current_pref_orient + if structure is not None: current_adp = tuple(atom.adp_type.value for atom in structure.atom_sites) if self._cached_adp_types.get(combined_name) != current_adp: @@ -693,6 +720,14 @@ def _update_experiment_in_cryspy_dict( cryspy_asymmetry[2] = experiment.peak.asym_empir_3.value cryspy_asymmetry[3] = experiment.peak.asym_empir_4.value + # Preferred orientation (March-Dollase): patch the + # refinable coefficient (g_1) and random fraction (g_2) + # in place, matched to each emitted texture row by phase + # label. h/k/l are fixed descriptors, so texture_axis is + # never patched. The keys are absent unless a texture + # loop was emitted, so guard. + _update_texture_in_cryspy_dict(cryspy_expt_dict, experiment) + elif experiment.type.beam_mode.value == BeamModeEnum.TIME_OF_FLIGHT: cryspy_expt_name = f'tof_{experiment.name}' cryspy_expt_dict = cryspy_dict[cryspy_expt_name] @@ -1026,6 +1061,7 @@ def _convert_experiment_to_cryspy_cif( # noqa: PLR6301 # Structure sections _cif_orient_matrix_section(cif_lines, expt_type) _cif_phase_section(cif_lines, expt_type, linked_structure) + _cif_pref_orient_section(cif_lines, expt_type, experiment, linked_structure) _cif_background_section(cif_lines, expt_type, twotheta_min, twotheta_max) # Measured data @@ -1297,6 +1333,99 @@ def _cif_phase_section( )) +def _cif_pref_orient_section( + cif_lines: list[str], + expt_type: object | None, + experiment: object, + linked_structure: object, +) -> None: + """ + Append the cryspy texture (March-Dollase) loop for the phase. + + cryspy keys texture to a phase by ``_texture_label``, so only the + ``pref_orient`` row whose ``phase_id`` matches the phase being + calculated is emitted. A row with ``r = 1`` is a mathematical no-op; + an empty collection (the default) emits nothing. + """ + # Initial support is constant-wavelength only (ADR Deferred Work); + # the TOF pass-through is not wired, so a TOF texture loop would + # go stale on refinement. Emit nothing for TOF to keep the scope + # consistent end to end. + if ( + expt_type is None + or expt_type.sample_form.value != SampleFormEnum.POWDER + or expt_type.beam_mode.value != BeamModeEnum.CONSTANT_WAVELENGTH + ): + return + pref_orient = getattr(experiment, 'preferred_orientation', None) + if pref_orient is None: + return + phase_label = linked_structure.name + row = next( + (item for item in pref_orient if item.phase_id.value == phase_label), + None, + ) + if row is None: + return + cif_lines.extend(( + '', + 'loop_', + '_texture_label', + '_texture_g_1', + '_texture_g_2', + '_texture_h_ax', + '_texture_k_ax', + '_texture_l_ax', + ( + f'{phase_label} {_march_r_to_cryspy_g1(row.march_r.value)} ' + f'{row.march_random_fract.value} ' + f'{row.index_h.value} {row.index_k.value} {row.index_l.value}' + ), + )) + + +def _march_r_to_cryspy_g1(r: float) -> float: + """ + Convert the IUCr/FullProf March coefficient to cryspy ``g_1``. + + CrysPy's "Modified March" parametrises March-Dollase with the + **reciprocal** coefficient ``g_1 = 1/r`` (verified against + FullProf). The user-facing ``r`` follows the standard + IUCr/FullProf/GSAS convention (1 = none, ``<1`` disk, ``>1`` needle) + and is inverted before it reaches the backend. CrysPy's factor is + also not volume-normalised, but that is a constant per-phase factor + absorbed by the scale (it slightly distorts the ``fraction``/``g_2`` + correspondence). + """ + return 1.0 / r + + +def _update_texture_in_cryspy_dict( + cryspy_expt_dict: dict[str, Any], + experiment: object, +) -> None: + """ + Patch cryspy texture g_1/g_2 from preferred-orientation rows. + + Matches each emitted texture row to a ``pref_orient`` row by phase + label and writes the refinable coefficient and random fraction in + place. ``index_h``/``index_k``/``index_l`` are fixed descriptors, so + ``texture_axis`` is never touched. No-op when no texture loop was + emitted. + """ + if 'texture_g1' not in cryspy_expt_dict: + return + pref_orient = getattr(experiment, 'preferred_orientation', None) + if pref_orient is None: + return + rows = {item.phase_id.value: item for item in pref_orient} + for index, label in enumerate(cryspy_expt_dict['texture_name']): + row = rows.get(str(label)) + if row is not None: + cryspy_expt_dict['texture_g1'][index] = _march_r_to_cryspy_g1(row.march_r.value) + cryspy_expt_dict['texture_g2'][index] = row.march_random_fract.value + + def _cif_background_section( cif_lines: list[str], expt_type: object | None, diff --git a/src/easydiffraction/datablocks/experiment/categories/pref_orient/__init__.py b/src/easydiffraction/datablocks/experiment/categories/pref_orient/__init__.py new file mode 100644 index 000000000..f5ab05c1a --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/pref_orient/__init__.py @@ -0,0 +1,8 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +""" +Preferred-orientation category (March-Dollase) for textured powders. +""" + +from easydiffraction.datablocks.experiment.categories.pref_orient.default import PrefOrient +from easydiffraction.datablocks.experiment.categories.pref_orient.default import PrefOrients diff --git a/src/easydiffraction/datablocks/experiment/categories/pref_orient/default.py b/src/easydiffraction/datablocks/experiment/categories/pref_orient/default.py new file mode 100644 index 000000000..9c1d74c50 --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/pref_orient/default.py @@ -0,0 +1,204 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +"""Per-phase March-Dollase preferred-orientation corrections.""" + +from __future__ import annotations + +from easydiffraction.core.category import CategoryCollection +from easydiffraction.core.category import CategoryItem +from easydiffraction.core.display_handler import DisplayHandler +from easydiffraction.core.metadata import CalculatorSupport +from easydiffraction.core.metadata import Compatibility +from easydiffraction.core.metadata import TypeInfo +from easydiffraction.core.validation import AttributeSpec +from easydiffraction.core.validation import RangeValidator +from easydiffraction.core.validation import RegexValidator +from easydiffraction.core.variable import IntegerDescriptor +from easydiffraction.core.variable import Parameter +from easydiffraction.core.variable import StringDescriptor +from easydiffraction.datablocks.experiment.categories.pref_orient.factory import PrefOrientFactory +from easydiffraction.datablocks.experiment.item.enums import CalculatorEnum +from easydiffraction.datablocks.experiment.item.enums import SampleFormEnum +from easydiffraction.datablocks.experiment.item.enums import ScatteringTypeEnum +from easydiffraction.io.cif.handler import CifHandler + + +class PrefOrient(CategoryItem): + """March-Dollase preferred-orientation correction for one phase.""" + + _category_code = 'pref_orient' + _category_entry_name = 'phase_id' + + def __init__(self) -> None: + super().__init__() + + self._phase_id = StringDescriptor( + name='phase_id', + description='Identifier of the corrected phase', + value_spec=AttributeSpec( + default='Si', + validator=RegexValidator(pattern=r'^[A-Za-z_][A-Za-z0-9_]*$'), + ), + cif_handler=CifHandler( + names=['_pref_orient.phase_id'], + iucr_name='_pd_pref_orient_March_Dollase.phase_id', + ), + display_handler=DisplayHandler( + display_name='Phase', + latex_name='Phase', + ), + ) + self._march_r = Parameter( + name='march_r', + description='March coefficient (1 = no preferred orientation).', + value_spec=AttributeSpec( + default=1.0, + validator=RangeValidator(gt=0.0), + ), + cif_handler=CifHandler( + names=['_pref_orient.march_r'], + iucr_name='_pd_pref_orient_March_Dollase.r', + ), + display_handler=DisplayHandler( + display_name='March coefficient', + latex_name='r', + ), + ) + self._index_h = IntegerDescriptor( + name='index_h', + description='Texture-axis Miller index h', + value_spec=AttributeSpec(default=0), + cif_handler=CifHandler( + names=['_pref_orient.index_h'], + iucr_name='_pd_pref_orient_March_Dollase.index_h', + ), + display_handler=DisplayHandler( + display_name='h', + latex_name='h', + ), + ) + self._index_k = IntegerDescriptor( + name='index_k', + description='Texture-axis Miller index k', + value_spec=AttributeSpec(default=0), + cif_handler=CifHandler( + names=['_pref_orient.index_k'], + iucr_name='_pd_pref_orient_March_Dollase.index_k', + ), + display_handler=DisplayHandler( + display_name='k', + latex_name='k', + ), + ) + self._index_l = IntegerDescriptor( + name='index_l', + description='Texture-axis Miller index l', + value_spec=AttributeSpec(default=1), + cif_handler=CifHandler( + names=['_pref_orient.index_l'], + iucr_name='_pd_pref_orient_March_Dollase.index_l', + ), + display_handler=DisplayHandler( + display_name='l', + latex_name='l', + ), + ) + self._march_random_fract = Parameter( + name='march_random_fract', + description='Random (untextured) fraction; 0 = pure March-Dollase.', + value_spec=AttributeSpec( + default=0.0, + validator=RangeValidator(ge=0.0, le=1.0), + ), + cif_handler=CifHandler( + names=['_pref_orient.march_random_fract'], + iucr_name='_easydiffraction_pref_orient.march_random_fract', + ), + display_handler=DisplayHandler( + display_name='Random fraction', + latex_name='fraction', + ), + ) + + # ------------------------------------------------------------------ + # Public properties + # ------------------------------------------------------------------ + + @property + def phase_id(self) -> StringDescriptor: + """Identifier of the corrected phase.""" + return self._phase_id + + @phase_id.setter + def phase_id(self, value: str) -> None: + self._phase_id.value = value + + @property + def march_r(self) -> Parameter: + """March coefficient (1 = no preferred orientation).""" + return self._march_r + + @march_r.setter + def march_r(self, value: float) -> None: + self._march_r.value = value + + # Miller indices use the ``index_h``/``index_k``/``index_l`` names + # already established by the ``refln`` categories. This also avoids + # a bare ambiguous ``l`` name (ruff E741/E743). + + @property + def index_h(self) -> IntegerDescriptor: + """Texture-axis Miller index h.""" + return self._index_h + + @index_h.setter + def index_h(self, value: int) -> None: + self._index_h.value = value + + @property + def index_k(self) -> IntegerDescriptor: + """Texture-axis Miller index k.""" + return self._index_k + + @index_k.setter + def index_k(self, value: int) -> None: + self._index_k.value = value + + @property + def index_l(self) -> IntegerDescriptor: + """Texture-axis Miller index l.""" + return self._index_l + + @index_l.setter + def index_l(self, value: int) -> None: + self._index_l.value = value + + @property + def march_random_fract(self) -> Parameter: + """Random (untextured) fraction; 0 = pure March-Dollase.""" + return self._march_random_fract + + @march_random_fract.setter + def march_random_fract(self, value: float) -> None: + self._march_random_fract.value = value + + +@PrefOrientFactory.register +class PrefOrients(CategoryCollection): + """Collection of per-phase preferred-orientation corrections.""" + + type_info = TypeInfo( + tag='default', + description='Per-phase March-Dollase preferred orientation', + ) + compatibility = Compatibility( + sample_form=frozenset({SampleFormEnum.POWDER}), + scattering_type=frozenset({ScatteringTypeEnum.BRAGG}), + ) + calculator_support = CalculatorSupport( + calculators=frozenset({CalculatorEnum.CRYSPY}), + ) + + def __init__(self) -> None: + """Create an empty collection of preferred-orientation rows.""" + super().__init__(item_type=PrefOrient) diff --git a/src/easydiffraction/datablocks/experiment/categories/pref_orient/factory.py b/src/easydiffraction/datablocks/experiment/categories/pref_orient/factory.py new file mode 100644 index 000000000..f1c357c21 --- /dev/null +++ b/src/easydiffraction/datablocks/experiment/categories/pref_orient/factory.py @@ -0,0 +1,19 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause +""" +Preferred-orientation factory — delegates entirely to ``FactoryBase``. +""" + +from __future__ import annotations + +from typing import ClassVar + +from easydiffraction.core.factory import FactoryBase + + +class PrefOrientFactory(FactoryBase): + """Create preferred-orientation collections by tag.""" + + _default_rules: ClassVar[dict] = { + frozenset(): 'default', + } diff --git a/src/easydiffraction/datablocks/experiment/item/base.py b/src/easydiffraction/datablocks/experiment/item/base.py index 77f92c218..3588681c3 100644 --- a/src/easydiffraction/datablocks/experiment/item/base.py +++ b/src/easydiffraction/datablocks/experiment/item/base.py @@ -97,6 +97,7 @@ def _attach_category_parents(self) -> None: getattr(self, '_instrument', None), getattr(self, '_refln', None), getattr(self, '_linked_phases', None), + getattr(self, '_pref_orient', None), getattr(self, '_excluded_regions', None), getattr(self, '_data', None), getattr(self, '_data_range', None), diff --git a/src/easydiffraction/datablocks/experiment/item/bragg_pd.py b/src/easydiffraction/datablocks/experiment/item/bragg_pd.py index 672a7c4c4..bc3573d32 100644 --- a/src/easydiffraction/datablocks/experiment/item/bragg_pd.py +++ b/src/easydiffraction/datablocks/experiment/item/bragg_pd.py @@ -12,6 +12,7 @@ from easydiffraction.core.metadata import TypeInfo from easydiffraction.datablocks.experiment.categories.background.factory import BackgroundFactory from easydiffraction.datablocks.experiment.categories.instrument.factory import InstrumentFactory +from easydiffraction.datablocks.experiment.categories.pref_orient.factory import PrefOrientFactory from easydiffraction.datablocks.experiment.categories.refln.factory import ReflnFactory from easydiffraction.datablocks.experiment.item.base import PdExperimentBase from easydiffraction.datablocks.experiment.item.enums import BeamModeEnum @@ -63,6 +64,7 @@ def __init__( ) self._instrument = InstrumentFactory.create(self._instrument_type) self._background = BackgroundFactory.create(BackgroundFactory.default_tag()) + self._pref_orient = PrefOrientFactory.create(PrefOrientFactory.default_tag()) self._refln = None self._sync_refln_category() self._attach_category_parents() @@ -187,6 +189,15 @@ def background(self) -> object: """Active background model for this experiment.""" return self._background + # ------------------------------------------------------------------ + # Preferred orientation (Bragg powder only) + # ------------------------------------------------------------------ + + @property + def preferred_orientation(self) -> object: + """Per-phase March-Dollase preferred-orientation corrections.""" + return self._pref_orient + def _restore_switchable_types(self, block: object) -> None: """ Restore Bragg powder switchable category types from CIF. diff --git a/src/easydiffraction/io/cif/iucr_writer.py b/src/easydiffraction/io/cif/iucr_writer.py index 761814245..da31df643 100644 --- a/src/easydiffraction/io/cif/iucr_writer.py +++ b/src/easydiffraction/io/cif/iucr_writer.py @@ -485,6 +485,7 @@ def _write_powder_pattern_block( _write_powder_pattern_refinement_section(lines, project) _write_powder_profile_loop(lines, experiment) _write_powder_refln_loop(lines, experiment) + _write_pref_orient_loop(lines, experiment) _write_powder_project_extensions(lines, experiment) return '\n'.join(lines) @@ -594,6 +595,64 @@ def _write_powder_refln_loop(lines: list[str], experiment: object) -> None: ) +def _write_pref_orient_loop(lines: list[str], experiment: object) -> None: + """ + Append the March-Dollase preferred-orientation loop. + + Standard fields use the IUCr ``_pd_pref_orient_March_Dollase.*`` + category (the ``.id`` serial is synthesised). The non-standard + random fraction (CrysPy ``g2``) is emitted under the project + namespace and only for rows whose fraction is non-zero, so the + common pure March-Dollase case produces a fully standard loop. + """ + rows = list(_collection_values(getattr(experiment, 'preferred_orientation', None))) + if not rows: + return + + _section(lines, 'Preferred orientation') + _write_loop( + lines, + ( + '_pd_pref_orient_March_Dollase.id', + '_pd_pref_orient_March_Dollase.phase_id', + '_pd_pref_orient_March_Dollase.index_h', + '_pd_pref_orient_March_Dollase.index_k', + '_pd_pref_orient_March_Dollase.index_l', + '_pd_pref_orient_March_Dollase.r', + '_pd_pref_orient_March_Dollase.r_su', + ), + [ + ( + str(index), + _attribute_value(row, 'phase_id'), + _attribute_value(row, 'index_h'), + _attribute_value(row, 'index_k'), + _attribute_value(row, 'index_l'), + _attribute_value(row, 'march_r'), + getattr(_attribute_descriptor(row, 'march_r'), 'uncertainty', None), + ) + for index, row in enumerate(rows, start=1) + ], + ) + + fraction_rows = [ + (str(index), _attribute_value(row, 'march_random_fract')) + for index, row in enumerate(rows, start=1) + if _attribute_value(row, 'march_random_fract') + ] + if not fraction_rows: + return + _section(lines, 'Preferred orientation random fraction') + _write_loop( + lines, + ( + '_easydiffraction_pref_orient.id', + '_easydiffraction_pref_orient.march_random_fract', + ), + fraction_rows, + ) + + def _write_powder_project_extensions(lines: list[str], experiment: object) -> None: """Append powder EasyDiffraction extension values.""" extension_rows = _powder_extension_items(experiment) diff --git a/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py b/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py index ddc866515..bfa5c1db8 100644 --- a/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py +++ b/tests/unit/easydiffraction/analysis/calculators/test_cryspy.py @@ -383,3 +383,106 @@ def test_temporarily_convert_to_u_notation_stashes_and_restores_beta(): assert aniso.adp_11.value == pytest.approx(0.001) assert aniso.adp_23.value == pytest.approx(-0.0002) assert '_atom_site_aniso.beta_11' in aniso.adp_11._cif_handler.names + + +def _bragg_powder_experiment(beam_mode): + """Build a real Bragg powder experiment with one PO row.""" + from easydiffraction import ExperimentFactory + + experiment = ExperimentFactory.from_scratch( + name='lbco', + sample_form='powder', + beam_mode=beam_mode, + radiation_probe='neutron', + scattering_type='bragg', + ) + experiment.preferred_orientation.create( + phase_id='lbco', march_r=0.5, index_h=0, index_k=0, index_l=1 + ) + return experiment + + +def test_cif_pref_orient_section_emits_for_constant_wavelength(): + import easydiffraction.analysis.calculators.cryspy as MUT + + experiment = _bragg_powder_experiment('constant wavelength') + structure = SimpleNamespace(name='lbco') + cif_lines: list[str] = [] + MUT._cif_pref_orient_section(cif_lines, experiment.type, experiment, structure) + text = '\n'.join(cif_lines) + + assert '_texture_g_1' in text + assert '_texture_label' in text + # The row's user-facing March coefficient r=0.5 maps to cryspy + # g_1 = 1/r = 2.0 (reciprocal convention). + assert 'lbco 2.0' in text + + +def test_cif_pref_orient_section_skips_time_of_flight(): + # TOF is Deferred Work: no texture loop is emitted (the TOF cached + # pass-through is not wired), so values cannot go stale. + import easydiffraction.analysis.calculators.cryspy as MUT + + experiment = _bragg_powder_experiment('time-of-flight') + structure = SimpleNamespace(name='lbco') + cif_lines: list[str] = [] + MUT._cif_pref_orient_section(cif_lines, experiment.type, experiment, structure) + + assert not any('_texture_g_1' in line for line in cif_lines) + + +def test_update_texture_in_cryspy_dict_patches_g1_and_g2(): + import easydiffraction.analysis.calculators.cryspy as MUT + + experiment = _bragg_powder_experiment('constant wavelength') + experiment.preferred_orientation['lbco'].march_r = 0.6 + experiment.preferred_orientation['lbco'].march_random_fract = 0.2 + + cryspy_expt_dict = { + 'texture_name': ['lbco'], + 'texture_g1': [1.0], + 'texture_g2': [0.0], + } + MUT._update_texture_in_cryspy_dict(cryspy_expt_dict, experiment) + + # r maps to cryspy g_1 = 1/r (reciprocal); fraction maps to g_2. + assert cryspy_expt_dict['texture_g1'][0] == pytest.approx(1.0 / 0.6) + assert cryspy_expt_dict['texture_g2'][0] == 0.2 + + +def test_update_texture_in_cryspy_dict_noop_without_texture_keys(): + import easydiffraction.analysis.calculators.cryspy as MUT + + experiment = _bragg_powder_experiment('constant wavelength') + cryspy_expt_dict = {'wavelength': [1.5]} + MUT._update_texture_in_cryspy_dict(cryspy_expt_dict, experiment) + + assert 'texture_g1' not in cryspy_expt_dict + + +def test_invalidate_stale_cache_drops_dict_on_pref_orient_axis_change(): + from easydiffraction.analysis.calculators.cryspy import CryspyCalculator + + experiment = _bragg_powder_experiment('constant wavelength') + calc = CryspyCalculator() + combined_name = 'lbco_lbco' + + # First pass records the peak/pref-orient signatures (and drops the + # cache because nothing was recorded yet); re-populate afterwards. + calc._invalidate_stale_cache(combined_name, experiment, None) + calc._cryspy_dicts[combined_name] = {'sentinel': True} + + # No change -> cache survives. + calc._invalidate_stale_cache(combined_name, experiment, None) + assert combined_name in calc._cryspy_dicts + + # Value-only edit must NOT invalidate. + experiment.preferred_orientation['lbco'].march_r = 2.0 + calc._invalidate_stale_cache(combined_name, experiment, None) + assert combined_name in calc._cryspy_dicts + + # Direction edit changes the signature and must drop the cache. + experiment.preferred_orientation['lbco'].index_l = 0 + experiment.preferred_orientation['lbco'].index_h = 1 + calc._invalidate_stale_cache(combined_name, experiment, None) + assert combined_name not in calc._cryspy_dicts diff --git a/tests/unit/easydiffraction/datablocks/experiment/categories/test_pref_orient.py b/tests/unit/easydiffraction/datablocks/experiment/categories/test_pref_orient.py new file mode 100644 index 000000000..64b123bed --- /dev/null +++ b/tests/unit/easydiffraction/datablocks/experiment/categories/test_pref_orient.py @@ -0,0 +1,155 @@ +# SPDX-FileCopyrightText: 2026 EasyScience contributors +# SPDX-License-Identifier: BSD-3-Clause + + +def test_module_import(): + import easydiffraction.datablocks.experiment.categories.pref_orient as MUT + + assert MUT.__name__.endswith('pref_orient') + + +def test_pref_orient_defaults_are_noop(): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrient + + po = PrefOrient() + assert po.march_r.value == 1.0 # March coefficient: no texture + assert po.march_random_fract.value == 0.0 # pure March-Dollase + assert (po.index_h.value, po.index_k.value, po.index_l.value) == (0, 0, 1) + assert po.phase_id.value == 'Si' + + +def test_pref_orient_property_setters(): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrient + + po = PrefOrient() + po.phase_id = 'lbco' + po.march_r = 0.75 + po.march_random_fract = 0.2 + po.index_h = 1 + po.index_k = 0 + po.index_l = 2 + + assert po.phase_id.value == 'lbco' + assert po.march_r.value == 0.75 + assert po.march_random_fract.value == 0.2 + assert (po.index_h.value, po.index_k.value, po.index_l.value) == (1, 0, 2) + + +def test_pref_orient_r_must_be_positive(monkeypatch): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrient + from easydiffraction.utils.logging import Logger + + monkeypatch.setattr(Logger, '_reaction', Logger.Reaction.WARN, raising=True) + + po = PrefOrient() + po.march_r = 0.0 # gt=0 -> rejected, keeps default + assert po.march_r.value == 1.0 + po.march_r = -0.5 + assert po.march_r.value == 1.0 + + +def test_pref_orient_fraction_within_unit_interval(monkeypatch): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrient + from easydiffraction.utils.logging import Logger + + monkeypatch.setattr(Logger, '_reaction', Logger.Reaction.WARN, raising=True) + + po = PrefOrient() + po.march_random_fract = 1.5 # le=1 -> rejected + assert po.march_random_fract.value == 0.0 + po.march_random_fract = -0.1 # ge=0 -> rejected + assert po.march_random_fract.value == 0.0 + po.march_random_fract = 0.5 # valid + assert po.march_random_fract.value == 0.5 + + +def test_pref_orients_create_and_default_cif(): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrients + + coll = PrefOrients() + coll.create(phase_id='lbco', march_r=0.8, index_h=0, index_k=0, index_l=1) + + cif = coll.as_cif + assert 'loop_' in cif + for tag in ( + '_pref_orient.phase_id', + '_pref_orient.march_r', + '_pref_orient.index_h', + '_pref_orient.index_k', + '_pref_orient.index_l', + '_pref_orient.march_random_fract', + ): + assert tag in cif + + +def test_pref_orient_factory_and_metadata(): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrients + from easydiffraction.datablocks.experiment.categories.pref_orient.factory import ( + PrefOrientFactory, + ) + from easydiffraction.datablocks.experiment.item.enums import CalculatorEnum + from easydiffraction.datablocks.experiment.item.enums import SampleFormEnum + from easydiffraction.datablocks.experiment.item.enums import ScatteringTypeEnum + + coll = PrefOrientFactory.create(PrefOrientFactory.default_tag()) + assert isinstance(coll, PrefOrients) + assert PrefOrients.type_info.tag == 'default' + assert SampleFormEnum.POWDER in PrefOrients.compatibility.sample_form + assert ScatteringTypeEnum.BRAGG in PrefOrients.compatibility.scattering_type + assert PrefOrients.calculator_support.supports(CalculatorEnum.CRYSPY) + assert not PrefOrients.calculator_support.supports(CalculatorEnum.PDFFIT) + + +def test_preferred_orientation_exposed_on_bragg_powder_only(): + from easydiffraction import ExperimentFactory + + bragg = ExperimentFactory.from_scratch( + name='bragg', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='bragg', + ) + assert hasattr(bragg, 'preferred_orientation') + bragg.preferred_orientation.create( + phase_id='bragg', march_r=0.5, index_h=0, index_k=0, index_l=1 + ) + # The collection is parent-linked to the experiment, enabling dirty + # tracking on row changes. + assert bragg.preferred_orientation._parent is bragg + + total = ExperimentFactory.from_scratch( + name='total', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='total', + ) + assert not hasattr(total, 'preferred_orientation') + + +def test_pref_orient_cif_round_trip(): + from easydiffraction import ExperimentFactory + + experiment = ExperimentFactory.from_scratch( + name='lbco', + sample_form='powder', + beam_mode='constant wavelength', + radiation_probe='neutron', + scattering_type='bragg', + ) + experiment.preferred_orientation.create( + phase_id='lbco', + march_r=0.75, + march_random_fract=0.2, + index_h=1, + index_k=0, + index_l=2, + ) + + restored = ExperimentFactory.from_cif_str(experiment.as_cif) + + row = restored.preferred_orientation['lbco'] + assert row.march_r.value == 0.75 + assert row.march_random_fract.value == 0.2 + assert (row.index_h.value, row.index_k.value, row.index_l.value) == (1, 0, 2) diff --git a/tests/unit/easydiffraction/io/cif/test_iucr_writer.py b/tests/unit/easydiffraction/io/cif/test_iucr_writer.py index 39c933a2f..ccffa8428 100644 --- a/tests/unit/easydiffraction/io/cif/test_iucr_writer.py +++ b/tests/unit/easydiffraction/io/cif/test_iucr_writer.py @@ -572,3 +572,35 @@ def test_atom_site_aniso_section_renders_beta_header_and_tags(): assert 'Anisotropic ADP (beta)' in text assert '_atom_site_aniso.beta_11' in text + + +def test_write_pref_orient_loop_standard_and_fraction(): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrients + from easydiffraction.io.cif import iucr_writer as W + + coll = PrefOrients() + coll.create(phase_id='lbco', march_r=0.75, index_h=0, index_k=0, index_l=1) # fraction=0 + experiment = SimpleNamespace(preferred_orientation=coll) + + lines: list[str] = [] + W._write_pref_orient_loop(lines, experiment) + text = '\n'.join(lines) + assert '_pd_pref_orient_March_Dollase.r' in text + assert '_pd_pref_orient_March_Dollase.index_l' in text + # fraction == 0 -> the non-standard namespaced item is omitted + assert '_easydiffraction_pref_orient.march_random_fract' not in text + + coll['lbco'].march_random_fract = 0.3 + lines2: list[str] = [] + W._write_pref_orient_loop(lines2, experiment) + assert '_easydiffraction_pref_orient.march_random_fract' in '\n'.join(lines2) + + +def test_write_pref_orient_loop_empty_is_noop(): + from easydiffraction.datablocks.experiment.categories.pref_orient import PrefOrients + from easydiffraction.io.cif import iucr_writer as W + + experiment = SimpleNamespace(preferred_orientation=PrefOrients()) + lines: list[str] = [] + W._write_pref_orient_loop(lines, experiment) + assert lines == []