diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 27a9f9543..7e6b7e68e 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -88,6 +88,13 @@ jobs: # Note: The gh-pages branch is fetched separately later for mike deployment. - name: Checkout repository uses: actions/checkout@v6 + with: + # Full history with tags so versioningit derives the real + # version (e.g. 0.18.0+dev40) instead of the v999.0.0 fallback + # (tool.versioningit.vcs default-tag), which would otherwise + # appear as "edi 999" in the executed notebook outputs rendered + # to HTML. + fetch-depth: 0 # Activate dark mode to create documentation with Plotly charts in dark mode # Need a better solution to automatically switch the chart colour theme based on the mkdocs material switcher diff --git a/.github/workflows/nightly-test.yml b/.github/workflows/nightly-test.yml index 9d605e425..25b36a4b7 100644 --- a/.github/workflows/nightly-test.yml +++ b/.github/workflows/nightly-test.yml @@ -27,6 +27,10 @@ jobs: steps: - name: Check-out repository uses: actions/checkout@v6 + with: + # Full history with tags so versioningit derives the real + # version instead of the v999.0.0 fallback in notebook output. + fetch-depth: 0 - name: Set up pixi uses: ./.github/actions/setup-pixi diff --git a/.github/workflows/tutorial-tests.yml b/.github/workflows/tutorial-tests.yml index 4e93a6383..42fe80241 100644 --- a/.github/workflows/tutorial-tests.yml +++ b/.github/workflows/tutorial-tests.yml @@ -41,6 +41,10 @@ jobs: steps: - name: Checkout repository uses: actions/checkout@v6 + with: + # Full history with tags so versioningit derives the real + # version instead of the v999.0.0 fallback in notebook output. + fetch-depth: 0 - name: Set up pixi uses: ./.github/actions/setup-pixi diff --git a/docs/dev/adrs/accepted/development-docs-structure.md b/docs/dev/adrs/accepted/development-docs-structure.md index b74abd317..dddc888c0 100644 --- a/docs/dev/adrs/accepted/development-docs-structure.md +++ b/docs/dev/adrs/accepted/development-docs-structure.md @@ -37,14 +37,19 @@ docs/dev/ | |-- accepted/ | `-- suggestions/ |-- issues/ -| |-- open.md -| `-- closed.md +| |-- index.md +| |-- open/ +| `-- closed/ |-- package-structure/ | |-- full.md | `-- short.md `-- plans/ ``` +Issues are one Markdown file per issue under `issues/open/` and +`issues/closed/`, with `issues/index.md` as the table of contents (not +flat `open.md` / `closed.md` files). + Use lowercase directory names for new development-doc folders. The feature/roadmap matrix is published directly in the user documentation at `docs/docs/features/index.md` (single source of truth for both diff --git a/docs/dev/adrs/accepted/edstar-project-persistence.md b/docs/dev/adrs/accepted/edstar-project-persistence.md index 27f8b2abd..f9ed7bf3b 100644 --- a/docs/dev/adrs/accepted/edstar-project-persistence.md +++ b/docs/dev/adrs/accepted/edstar-project-persistence.md @@ -437,6 +437,13 @@ For type-neutral ADPs, `edi_names` stays the neutral `_atom_site.adp_iso` (so the Edi save is always type-neutral) while the type-specific B/U order is applied to `cif_names` for export. +The "generated inventory" referenced throughout this ADR (the full set +of `TagSpec`/`CifHandler` entries used as the migration and +parameter-docs audit) is produced by +[`tools/edi_handler_inventory.py`](../../../../tools/edi_handler_inventory.py) +and written to the sidecar `handler-inventory.json` next to this file. +Regenerate it with that tool rather than hand-editing the JSON. + ## Consequences ### Positive diff --git a/docs/dev/adrs/accepted/minimizer-category-consolidation.md b/docs/dev/adrs/accepted/minimizer-category-consolidation.md index 39cf44b33..ac8a196b2 100644 --- a/docs/dev/adrs/accepted/minimizer-category-consolidation.md +++ b/docs/dev/adrs/accepted/minimizer-category-consolidation.md @@ -115,7 +115,7 @@ owner, category as a read-only attribute that gets swapped. ### 3. Per-parameter posterior data lives on `Parameter.posterior` Adopt the proposal from -[`parameter-posterior-summary.md`](../suggestions/parameter-posterior-summary.md): +[`parameter-posterior-summary.md`](parameter-posterior-summary.md): `GenericParameter.posterior` is `None` for deterministic fits and a `PosteriorParameterSummary` for Bayesian fits. The `_bayesian_parameter_posterior` CIF loop is removed; posterior summary @@ -466,9 +466,9 @@ category's class-level `_engine_metadata` dict. ### Suggestions superseded or absorbed -- [`parameter-posterior-summary.md`](../suggestions/parameter-posterior-summary.md) - — absorbed by §3 of this ADR. When this ADR is accepted, that - suggestion can be closed and a pointer added. +- [`parameter-posterior-summary.md`](parameter-posterior-summary.md) — + absorbed by §3 of this ADR. When this ADR is accepted, that suggestion + can be closed and a pointer added. ## Alternatives Considered diff --git a/docs/dev/adrs/suggestions/parameter-posterior-summary.md b/docs/dev/adrs/accepted/parameter-posterior-summary.md similarity index 100% rename from docs/dev/adrs/suggestions/parameter-posterior-summary.md rename to docs/dev/adrs/accepted/parameter-posterior-summary.md diff --git a/docs/dev/adrs/accepted/peak-profile-cutoff.md b/docs/dev/adrs/accepted/peak-profile-cutoff.md index 05778ee49..20a4fa1cd 100644 --- a/docs/dev/adrs/accepted/peak-profile-cutoff.md +++ b/docs/dev/adrs/accepted/peak-profile-cutoff.md @@ -46,7 +46,7 @@ unsafe (too aggressive for some data). Users therefore need a per- experiment knob, mirroring FullProf's `.pcr` `WDT`. This relates to the upstream capability-request workflow -([`upstream-capability-request-evidence.md`](../suggestions/upstream-capability-request-evidence.md)): +([`upstream-capability-request-evidence.md`](upstream-capability-request-evidence.md)): the literal cutoff was proposed upstream and released in cryspy 0.12.0, so EasyDiffraction drives it through the released `profile_cutoff_fwhm` key without requiring a cryspy CIF-schema change. diff --git a/docs/dev/adrs/suggestions/upstream-capability-request-evidence.md b/docs/dev/adrs/accepted/upstream-capability-request-evidence.md similarity index 99% rename from docs/dev/adrs/suggestions/upstream-capability-request-evidence.md rename to docs/dev/adrs/accepted/upstream-capability-request-evidence.md index 89f7e91ce..37339ba88 100644 --- a/docs/dev/adrs/suggestions/upstream-capability-request-evidence.md +++ b/docs/dev/adrs/accepted/upstream-capability-request-evidence.md @@ -2,7 +2,7 @@ ## Status -Proposed. +Accepted. ## Date diff --git a/docs/dev/adrs/suggestions/verification-example-lifecycle.md b/docs/dev/adrs/accepted/verification-example-lifecycle.md similarity index 99% rename from docs/dev/adrs/suggestions/verification-example-lifecycle.md rename to docs/dev/adrs/accepted/verification-example-lifecycle.md index ae5ee33eb..0158a698b 100644 --- a/docs/dev/adrs/suggestions/verification-example-lifecycle.md +++ b/docs/dev/adrs/accepted/verification-example-lifecycle.md @@ -2,7 +2,7 @@ ## Status -Proposed. +Accepted. ## Date diff --git a/docs/dev/adrs/index.md b/docs/dev/adrs/index.md index 04105e862..5b76a2869 100644 --- a/docs/dev/adrs/index.md +++ b/docs/dev/adrs/index.md @@ -13,65 +13,68 @@ folders. ## ADR Index -| Group | Status | Title | Short description | Link | -| -------------------- | ---------- | --------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------ | -| Analysis and fitting | Accepted | Fit Mode Categories and Fit Execution API | Splits fitting configuration from execution and defines active sibling fit-mode categories. | [`fit-mode-categories.md`](accepted/fit-mode-categories.md) | -| Analysis and fitting | Accepted | Runtime Fit Results | Keeps full fit outputs runtime-only in the current design unless a narrower persistence ADR is accepted. | [`runtime-fit-results.md`](accepted/runtime-fit-results.md) | -| Analysis and fitting | Accepted | Analysis CIF Fit State | Defines the persisted fit-state projection in `analysis/analysis.cif` and `analysis/mcmc.h5`. | [`analysis-cif-fit-state.md`](accepted/analysis-cif-fit-state.md) | -| Analysis and fitting | Accepted | Parameter Correlation Persistence | Persists deterministic and posterior correlation summaries in `_fit_parameter_correlation` | [`parameter-correlation-persistence.md`](accepted/parameter-correlation-persistence.md) | -| Analysis and fitting | Suggestion | Fit Output Files and Data Exports | Narrows remaining archive/export questions after adopting `results.csv` and `mcmc.h5`. | [`fit-output-files-and-data-exports.md`](suggestions/fit-output-files-and-data-exports.md) | -| Analysis and fitting | Accepted | Dataset-Driven Fit Mode Availability | Offers fit modes by per-mode preconditions, restricts `single` to one dataset (closing issue 85), and keeps `sequential` as the folder sweep. | [`dataset-driven-fit-modes.md`](accepted/dataset-driven-fit-modes.md) | -| Analysis and fitting | Accepted | Minimizer Category Consolidation | Collapses the seven Bayesian categories into one owner-level switchable `minimizer` category with HDF5 sidecar. | [`minimizer-category-consolidation.md`](accepted/minimizer-category-consolidation.md) | -| Analysis and fitting | Accepted | Minimizer Input/Output Split | Keeps `analysis.minimizer` input-only and moves scalar fit outputs to paired `analysis.fit_result` classes. | [`minimizer-input-output-split.md`](accepted/minimizer-input-output-split.md) | -| Analysis and fitting | Superseded | Parameter-Level Posterior Projection | Superseded by minimizer-category consolidation; kept as historical context for `parameter.posterior`. | [`parameter-posterior-summary.md`](suggestions/parameter-posterior-summary.md) | -| Analysis and fitting | Accepted | Undo Fit | Builds rollback semantics and CLI behavior on already-persisted pre-fit scalar snapshots. | [`undo-fit.md`](accepted/undo-fit.md) | -| Analysis and fitting | Accepted | Bayesian Resume and MCMC Sidecar Naming | Extends bumps-DREAM with resume/extend like emcee and renames the MCMC sidecar to `mcmc.h5` with per-engine state groups. | [`bayesian-resume-and-mcmc-sidecar.md`](accepted/bayesian-resume-and-mcmc-sidecar.md) | -| Analysis and fitting | Accepted | Post-Calculation Corrections Package | Moves calculator-independent corrections (absorption, polarization) into `analysis/corrections/`, separate from the calculation backends. | [`post-calculation-corrections-package.md`](accepted/post-calculation-corrections-package.md) | -| Core model | Accepted | Category Owners and Real Datablocks | Introduces `CategoryOwner` so singleton sections do not pretend to be real CIF datablocks. | [`category-owner-sections.md`](accepted/category-owner-sections.md) | -| Core model | Accepted | Enum-Backed Closed Value Sets | Requires finite option sets to use `(str, Enum)` classes for validation and dispatch. | [`enum-backed-closed-values.md`](accepted/enum-backed-closed-values.md) | -| Core model | Accepted | Guarded Public Properties | Uses property setters as the public writability contract for guarded objects. | [`guarded-public-properties.md`](accepted/guarded-public-properties.md) | -| Core model | Accepted | Two-Level Category Parameter Access | Keeps parameter access to `datablock.category.parameter` or `datablock.collection[id].parameter`. | [`category-parameter-access.md`](accepted/category-parameter-access.md) | -| Documentation | Accepted | Descriptor Property Docstring Template | Makes descriptor metadata the source of truth for public property docstrings and annotations. | [`property-docstring-template.md`](accepted/property-docstring-template.md) | -| Documentation | Accepted | Development Documentation Structure | Defines the `docs/dev` layout for ADRs, issues, plans, package structure, and roadmap. | [`development-docs-structure.md`](accepted/development-docs-structure.md) | -| Documentation | Accepted | Help Method Discoverability | Requires primary public objects and facades to expose consistent `help()` output. | [`help-discoverability.md`](accepted/help-discoverability.md) | -| Documentation | Accepted | Notebook Generation Source of Truth | Treats tutorial `.py` files as editable sources and notebooks as generated artifacts. | [`notebook-generation.md`](accepted/notebook-generation.md) | -| Documentation | Accepted | Plotting & Docs Performance for Interactive Figures | Self-hosts a lazy, shared figure runtime so docs pages load fast and progressively while staying interactive. | [`plotting-docs-performance.md`](accepted/plotting-docs-performance.md) | -| Documentation | Accepted | Documentation CI and Build Verification | Strict MkDocs builds, API-derived docs, snippet smoke tests, link checks, and prose/spelling checks. | [`documentation-ci-build.md`](accepted/documentation-ci-build.md) | -| Documentation | Accepted | Data Download Source Pinning | Pins downloadable data to one git commit kept in a packaged file, drops the redundant index checksum, cache-busting by commit-named index. | [`data-source-pinning.md`](accepted/data-source-pinning.md) | -| 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) | -| Experiment model | Accepted | Model Sample Absorption (Debye–Scherrer, μR) | Switchable `absorption` category applying a calculator-independent cylindrical Hewat A(θ) envelope for powder samples. | [`model-sample-absorption.md`](accepted/model-sample-absorption.md) | -| Experiment model | Accepted | X-ray CW Polarization Optics | Adds discoverable X-ray CW powder instrument fields for FullProf/Cryspy Lorentz-polarization and monochromator optics. | [`xray-cw-polarization-optics.md`](accepted/xray-cw-polarization-optics.md) | -| Experiment model | Accepted | Peak-Profile Range Cutoff (`cutoff_fwhm`) | Per-experiment literal peak-range cutoff (FullProf "WDT", cryspy 0.12.0); `cutoff_fwhm = 0` (default) computes the full range, a positive value skips the negligible far field to speed the cryspy profile. | [`peak-profile-cutoff.md`](accepted/peak-profile-cutoff.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) | -| Naming | Accepted | Downloadable Resource Naming | Replaces integer dataset/tutorial ids with stable descriptive slugs and moves presentation order into separate metadata. | [`resource-naming.md`](accepted/resource-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) | -| Persistence | Accepted | Loop Category Keys and Identity Naming | Documents loop collection keys and naming rules aligned with CIF category keys. | [`loop-category-key-identity.md`](accepted/loop-category-key-identity.md) | -| Persistence | Accepted | Project Facade and Persistence Layout | Documents the current `Project` facade and saved directory layout. | [`project-facade-and-persistence.md`](accepted/project-facade-and-persistence.md) | -| Persistence | Accepted | IUCr CIF Tag Alignment | Aligns default CIF tags with IUCr dictionaries and adds a clean IUCr-aligned report export. | [`iucr-cif-tag-alignment.md`](accepted/iucr-cif-tag-alignment.md) | -| Persistence | Accepted | Python and CIF Category Correspondence | Compares current Python paths and CIF tags, then records scoped one-to-one mapping for project-level categories. | [`python-cif-category-correspondence.md`](accepted/python-cif-category-correspondence.md) | -| Persistence | Accepted | Edi Project Persistence | Defines STAR-based EasyDiffraction project files with UX-oriented names and strict CIF reserved for report export. | [`edstar-project-persistence.md`](accepted/edstar-project-persistence.md) | -| Quality | Accepted | Lint Complexity Thresholds | Treats ruff PLR complexity limits as design guardrails that should not be bypassed. | [`lint-complexity-thresholds.md`](accepted/lint-complexity-thresholds.md) | -| Quality | Accepted | Lint Rule Scope and Test-File Exceptions | Records the standing tests/\*\* PLR/N812 ignores and CIF-aligned `id`/`type` builtin exception from the lint audit. | [`lint-rule-exceptions.md`](accepted/lint-rule-exceptions.md) | -| Quality | Accepted | Test Strategy | Defines layered unit, functional, integration, script, and notebook testing. | [`test-strategy.md`](accepted/test-strategy.md) | -| Quality | Accepted | Test Suite and Validation Strategy | Strict test layers, cost tiers, coverage/codecov policy, cross-engine verification docs, and a nightly validation harness. | [`test-suite-and-validation.md`](accepted/test-suite-and-validation.md) | -| Quality | Accepted | Notebook-Owned Verification Regression Gating | Replaces the external `ci_skip.txt` list with a single in-notebook `known_discrepancy` flag (plus a cell tag for pre-flag crashes). | [`verification-regression-flag.md`](accepted/verification-regression-flag.md) | -| Quality | Accepted | Software Version Labels on Verification Pages | Shows FullProf, EasyDiffraction, and engine versions on every verification page (e.g. `edi X.Y.Z (cryspy X.Y.Z)`) via a `verify` helper. | [`verification-software-version-labels.md`](accepted/verification-software-version-labels.md) | -| Quality | Suggestion | Verification Example Lifecycle | Defines naming, scope, reference-file, documentation, fit-section, and diagnostic-page conventions for future Verification examples. | [`verification-example-lifecycle.md`](suggestions/verification-example-lifecycle.md) | -| Quality | Suggestion | Upstream Capability Request Evidence | Defines reproducible request packets with source audits, parameter snippets, scripts, and screenshots for upstream Python API gaps. | [`upstream-capability-request-evidence.md`](suggestions/upstream-capability-request-evidence.md) | -| Structure model | Accepted | Type-Neutral ADP Parameters | Keeps ADP parameter object identities stable across B/U and iso/ani switches. | [`type-neutral-adp-parameters.md`](accepted/type-neutral-adp-parameters.md) | -| Structure model | Accepted | Automatic Wyckoff Position Detection | Detects Wyckoff letter, multiplicity, and site symmetry from space group and coordinates; calculators consume them. | [`wyckoff-letter-detection.md`](accepted/wyckoff-letter-detection.md) | -| Structure model | Accepted | Complete Space-Group Reference Database | One-time build of a complete space_groups.json.gz (all 230 groups) from cctbx, verified against multiple sources. | [`space-group-database.md`](accepted/space-group-database.md) | -| User-facing API | Accepted | Crystal Structure 3D Visualization | Adds a renderer-neutral scene model drawn by ASCII and interactive Three.js engines for viewing crystal structures. | [`crysview-structure-visualization.md`](accepted/crysview-structure-visualization.md) | -| User-facing API | Accepted | Display UX Facade | Defines `project.display` and `project.rendering` responsibilities and display method names. | [`display-ux.md`](accepted/display-ux.md) | -| User-facing API | Accepted | Fit Results Display Naming | Short, IUCr/GUM-aligned column headers (`s.u.`, `value`, `95% CI`) with a footnote glossary on every fit table. | [`fit-results-display-naming.md`](accepted/fit-results-display-naming.md) | -| User-facing API | Accepted | Project Summary Rendering | Defines project report configuration plus terminal, HTML, TeX, PDF, and clean report-CIF metadata policy. | [`project-summary-rendering.md`](accepted/project-summary-rendering.md) | -| User-facing API | Accepted | Selector Families | Distinguishes backend selectors, switchable-category selectors, and active-sibling selectors. | [`selector-families.md`](accepted/selector-families.md) | -| User-facing API | Accepted | String Paths and Live Descriptors | Separates persisted field selectors from references to live model parameters. | [`string-paths-and-live-descriptors.md`](accepted/string-paths-and-live-descriptors.md) | -| User-facing API | Accepted | Switchable Category API | Places multi-type category selectors on the owner and omits public selectors for fixed or single-type categories. | [`switchable-category-api.md`](accepted/switchable-category-api.md) | -| User-facing API | Accepted | Switchable Category Owned Selectors | Moves the writable `type` selector and `show_supported()` onto the category itself; collapses the CIF duplication. | [`switchable-category-owned-selectors.md`](accepted/switchable-category-owned-selectors.md) | -| User-facing API | Accepted | Unified Pattern View | `pattern()` always renders available data, drops `include`, and unifies single- and three-panel figure sizing. | [`pattern-display-unification.md`](accepted/pattern-display-unification.md) | -| User-facing API | Accepted | Value-Selector Discovery | Gives enumerated value fields a per-descriptor `show_supported()`, beside the three category-level selector families. | [`value-selector-discovery.md`](accepted/value-selector-discovery.md) | +| Group | Status | Title | Short description | Link | +| -------------------- | ---------- | --------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------- | +| Analysis and fitting | Accepted | Fit Mode Categories and Fit Execution API | Splits fitting configuration from execution and defines active sibling fit-mode categories. | [`fit-mode-categories.md`](accepted/fit-mode-categories.md) | +| Analysis and fitting | Accepted | Runtime Fit Results | Keeps full fit outputs runtime-only in the current design unless a narrower persistence ADR is accepted. | [`runtime-fit-results.md`](accepted/runtime-fit-results.md) | +| Analysis and fitting | Accepted | Analysis CIF Fit State | Defines the persisted fit-state projection in `analysis/analysis.cif` and `analysis/mcmc.h5`. | [`analysis-cif-fit-state.md`](accepted/analysis-cif-fit-state.md) | +| Analysis and fitting | Accepted | Parameter Correlation Persistence | Persists deterministic and posterior correlation summaries in `_fit_parameter_correlation` | [`parameter-correlation-persistence.md`](accepted/parameter-correlation-persistence.md) | +| Analysis and fitting | Suggestion | Fit Output Files and Data Exports | Narrows remaining archive/export questions after adopting `results.csv` and `mcmc.h5`. | [`fit-output-files-and-data-exports.md`](suggestions/fit-output-files-and-data-exports.md) | +| Analysis and fitting | Accepted | Dataset-Driven Fit Mode Availability | Offers fit modes by per-mode preconditions, restricts `single` to one dataset (closing issue 85), and keeps `sequential` as the folder sweep. | [`dataset-driven-fit-modes.md`](accepted/dataset-driven-fit-modes.md) | +| Analysis and fitting | Accepted | Minimizer Category Consolidation | Collapses the seven Bayesian categories into one owner-level switchable `minimizer` category with HDF5 sidecar. | [`minimizer-category-consolidation.md`](accepted/minimizer-category-consolidation.md) | +| Analysis and fitting | Accepted | Minimizer Input/Output Split | Keeps `analysis.minimizer` input-only and moves scalar fit outputs to paired `analysis.fit_result` classes. | [`minimizer-input-output-split.md`](accepted/minimizer-input-output-split.md) | +| Analysis and fitting | Superseded | Parameter-Level Posterior Projection | Superseded by minimizer-category consolidation; kept as historical context for `parameter.posterior`. | [`parameter-posterior-summary.md`](accepted/parameter-posterior-summary.md) | +| Analysis and fitting | Accepted | Undo Fit | Builds rollback semantics and CLI behavior on already-persisted pre-fit scalar snapshots. | [`undo-fit.md`](accepted/undo-fit.md) | +| Analysis and fitting | Accepted | Bayesian Resume and MCMC Sidecar Naming | Extends bumps-DREAM with resume/extend like emcee and renames the MCMC sidecar to `mcmc.h5` with per-engine state groups. | [`bayesian-resume-and-mcmc-sidecar.md`](accepted/bayesian-resume-and-mcmc-sidecar.md) | +| Analysis and fitting | Accepted | Post-Calculation Corrections Package | Moves calculator-independent corrections (absorption, polarization) into `analysis/corrections/`, separate from the calculation backends. | [`post-calculation-corrections-package.md`](accepted/post-calculation-corrections-package.md) | +| Analysis and fitting | Suggestion | In-House Diffraction Calculation Engine | Proposes a native diffraction calculation engine alongside the external backends. | [`in-house-calculation-engine.md`](suggestions/in-house-calculation-engine.md) | +| Core model | Accepted | Category Owners and Real Datablocks | Introduces `CategoryOwner` so singleton sections do not pretend to be real CIF datablocks. | [`category-owner-sections.md`](accepted/category-owner-sections.md) | +| Core model | Accepted | Enum-Backed Closed Value Sets | Requires finite option sets to use `(str, Enum)` classes for validation and dispatch. | [`enum-backed-closed-values.md`](accepted/enum-backed-closed-values.md) | +| Core model | Accepted | Guarded Public Properties | Uses property setters as the public writability contract for guarded objects. | [`guarded-public-properties.md`](accepted/guarded-public-properties.md) | +| Core model | Accepted | Two-Level Category Parameter Access | Keeps parameter access to `datablock.category.parameter` or `datablock.collection[id].parameter`. | [`category-parameter-access.md`](accepted/category-parameter-access.md) | +| Core model | Suggestion | Meaningful Numeric Precision in CIF Serialization | Serializes numeric CIF values at meaningful precision instead of full float repr. | [`cif-numeric-precision.md`](suggestions/cif-numeric-precision.md) | +| Core model | Suggestion | Lazy Pattern Recalculation | Recomputes patterns lazily via a per-experiment dirty flag instead of explicit updates. | [`lazy-pattern-recalculation.md`](suggestions/lazy-pattern-recalculation.md) | +| Documentation | Accepted | Descriptor Property Docstring Template | Makes descriptor metadata the source of truth for public property docstrings and annotations. | [`property-docstring-template.md`](accepted/property-docstring-template.md) | +| Documentation | Accepted | Development Documentation Structure | Defines the `docs/dev` layout for ADRs, issues, plans, package structure, and roadmap. | [`development-docs-structure.md`](accepted/development-docs-structure.md) | +| Documentation | Accepted | Help Method Discoverability | Requires primary public objects and facades to expose consistent `help()` output. | [`help-discoverability.md`](accepted/help-discoverability.md) | +| Documentation | Accepted | Notebook Generation Source of Truth | Treats tutorial `.py` files as editable sources and notebooks as generated artifacts. | [`notebook-generation.md`](accepted/notebook-generation.md) | +| Documentation | Accepted | Plotting & Docs Performance for Interactive Figures | Self-hosts a lazy, shared figure runtime so docs pages load fast and progressively while staying interactive. | [`plotting-docs-performance.md`](accepted/plotting-docs-performance.md) | +| Documentation | Accepted | Documentation CI and Build Verification | Strict MkDocs builds, API-derived docs, snippet smoke tests, link checks, and prose/spelling checks. | [`documentation-ci-build.md`](accepted/documentation-ci-build.md) | +| Documentation | Accepted | Data Download Source Pinning | Pins downloadable data to one git commit kept in a packaged file, drops the redundant index checksum, cache-busting by commit-named index. | [`data-source-pinning.md`](accepted/data-source-pinning.md) | +| 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) | +| Experiment model | Accepted | Model Sample Absorption (Debye–Scherrer, μR) | Switchable `absorption` category applying a calculator-independent cylindrical Hewat A(θ) envelope for powder samples. | [`model-sample-absorption.md`](accepted/model-sample-absorption.md) | +| Experiment model | Accepted | X-ray CW Polarization Optics | Adds discoverable X-ray CW powder instrument fields for FullProf/Cryspy Lorentz-polarization and monochromator optics. | [`xray-cw-polarization-optics.md`](accepted/xray-cw-polarization-optics.md) | +| Experiment model | Accepted | Peak-Profile Range Cutoff (`cutoff_fwhm`) | Per-experiment literal peak-range cutoff (FullProf "WDT", cryspy 0.12.0); `cutoff_fwhm = 0` (default) computes the full range, a positive value skips the negligible far field to speed the cryspy profile. | [`peak-profile-cutoff.md`](accepted/peak-profile-cutoff.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) | +| Naming | Accepted | Downloadable Resource Naming | Replaces integer dataset/tutorial ids with stable descriptive slugs and moves presentation order into separate metadata. | [`resource-naming.md`](accepted/resource-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) | +| Persistence | Accepted | Loop Category Keys and Identity Naming | Documents loop collection keys and naming rules aligned with CIF category keys. | [`loop-category-key-identity.md`](accepted/loop-category-key-identity.md) | +| Persistence | Accepted | Project Facade and Persistence Layout | Documents the current `Project` facade and saved directory layout. | [`project-facade-and-persistence.md`](accepted/project-facade-and-persistence.md) | +| Persistence | Accepted | IUCr CIF Tag Alignment | Aligns default CIF tags with IUCr dictionaries and adds a clean IUCr-aligned report export. | [`iucr-cif-tag-alignment.md`](accepted/iucr-cif-tag-alignment.md) | +| Persistence | Accepted | Python and CIF Category Correspondence | Compares current Python paths and CIF tags, then records scoped one-to-one mapping for project-level categories. | [`python-cif-category-correspondence.md`](accepted/python-cif-category-correspondence.md) | +| Persistence | Accepted | Edi Project Persistence | Defines STAR-based EasyDiffraction project files with UX-oriented names and strict CIF reserved for report export. | [`edstar-project-persistence.md`](accepted/edstar-project-persistence.md) | +| Quality | Accepted | Lint Complexity Thresholds | Treats ruff PLR complexity limits as design guardrails that should not be bypassed. | [`lint-complexity-thresholds.md`](accepted/lint-complexity-thresholds.md) | +| Quality | Accepted | Lint Rule Scope and Test-File Exceptions | Records the standing tests/\*\* PLR/N812 ignores and CIF-aligned `id`/`type` builtin exception from the lint audit. | [`lint-rule-exceptions.md`](accepted/lint-rule-exceptions.md) | +| Quality | Accepted | Test Strategy | Defines layered unit, functional, integration, script, and notebook testing. | [`test-strategy.md`](accepted/test-strategy.md) | +| Quality | Accepted | Test Suite and Validation Strategy | Strict test layers, cost tiers, coverage/codecov policy, cross-engine verification docs, and a nightly validation harness. | [`test-suite-and-validation.md`](accepted/test-suite-and-validation.md) | +| Quality | Accepted | Notebook-Owned Verification Regression Gating | Replaces the external `ci_skip.txt` list with a single in-notebook `known_discrepancy` flag (plus a cell tag for pre-flag crashes). | [`verification-regression-flag.md`](accepted/verification-regression-flag.md) | +| Quality | Accepted | Software Version Labels on Verification Pages | Shows FullProf, EasyDiffraction, and engine versions on every verification page (e.g. `edi X.Y.Z (cryspy X.Y.Z)`) via a `verify` helper. | [`verification-software-version-labels.md`](accepted/verification-software-version-labels.md) | +| Quality | Accepted | Verification Example Lifecycle | Defines naming, scope, reference-file, documentation, fit-section, and diagnostic-page conventions for future Verification examples. | [`verification-example-lifecycle.md`](accepted/verification-example-lifecycle.md) | +| Quality | Accepted | Upstream Capability Request Evidence | Defines reproducible request packets with source audits, parameter snippets, scripts, and screenshots for upstream Python API gaps. | [`upstream-capability-request-evidence.md`](accepted/upstream-capability-request-evidence.md) | +| Structure model | Accepted | Type-Neutral ADP Parameters | Keeps ADP parameter object identities stable across B/U and iso/ani switches. | [`type-neutral-adp-parameters.md`](accepted/type-neutral-adp-parameters.md) | +| Structure model | Accepted | Automatic Wyckoff Position Detection | Detects Wyckoff letter, multiplicity, and site symmetry from space group and coordinates; calculators consume them. | [`wyckoff-letter-detection.md`](accepted/wyckoff-letter-detection.md) | +| Structure model | Accepted | Complete Space-Group Reference Database | One-time build of a complete space_groups.json.gz (all 230 groups) from cctbx, verified against multiple sources. | [`space-group-database.md`](accepted/space-group-database.md) | +| User-facing API | Accepted | Crystal Structure 3D Visualization | Adds a renderer-neutral scene model drawn by ASCII and interactive Three.js engines for viewing crystal structures. | [`crysview-structure-visualization.md`](accepted/crysview-structure-visualization.md) | +| User-facing API | Accepted | Display UX Facade | Defines `project.display` and `project.rendering` responsibilities and display method names. | [`display-ux.md`](accepted/display-ux.md) | +| User-facing API | Accepted | Fit Results Display Naming | Short, IUCr/GUM-aligned column headers (`s.u.`, `value`, `95% CI`) with a footnote glossary on every fit table. | [`fit-results-display-naming.md`](accepted/fit-results-display-naming.md) | +| User-facing API | Accepted | Project Summary Rendering | Defines project report configuration plus terminal, HTML, TeX, PDF, and clean report-CIF metadata policy. | [`project-summary-rendering.md`](accepted/project-summary-rendering.md) | +| User-facing API | Accepted | Selector Families | Distinguishes backend selectors, switchable-category selectors, and active-sibling selectors. | [`selector-families.md`](accepted/selector-families.md) | +| User-facing API | Accepted | String Paths and Live Descriptors | Separates persisted field selectors from references to live model parameters. | [`string-paths-and-live-descriptors.md`](accepted/string-paths-and-live-descriptors.md) | +| User-facing API | Accepted | Switchable Category API | Places multi-type category selectors on the owner and omits public selectors for fixed or single-type categories. | [`switchable-category-api.md`](accepted/switchable-category-api.md) | +| User-facing API | Accepted | Switchable Category Owned Selectors | Moves the writable `type` selector and `show_supported()` onto the category itself; collapses the CIF duplication. | [`switchable-category-owned-selectors.md`](accepted/switchable-category-owned-selectors.md) | +| User-facing API | Accepted | Unified Pattern View | `pattern()` always renders available data, drops `include`, and unifies single- and three-panel figure sizing. | [`pattern-display-unification.md`](accepted/pattern-display-unification.md) | +| User-facing API | Accepted | Value-Selector Discovery | Gives enumerated value fields a per-descriptor `show_supported()`, beside the three category-level selector families. | [`value-selector-discovery.md`](accepted/value-selector-discovery.md) | diff --git a/docs/dev/issues/closed/add-single-crystal-tof-fit-verification-example.md b/docs/dev/issues/closed/add-single-crystal-tof-fit-verification-example.md new file mode 100644 index 000000000..dcabd6af9 --- /dev/null +++ b/docs/dev/issues/closed/add-single-crystal-tof-fit-verification-example.md @@ -0,0 +1,18 @@ +# 190. Add a Single-Crystal TOF Fit Verification Example + +**Closed:** added the single-crystal time-of-flight verification example +`docs/docs/verification/sc-neut-tof_taurine_basic.py` (and generated +`.ipynb`), built from a FullProf reference for Taurine (P 2₁/c, neutron +TOF single-crystal data, SENJU @ J-PARC). + +The FullProf model has extinction set to zero (Ext1 = 0, unrefined) so +the comparison focuses on the structure-factor physics shared by cryspy +and FullProf. After refining the overall scale only, edi-cryspy matches +the FullProf F²cal to ~0.01% (profile diff and max deviation), with area +ratio 1.0000 and shape correlation 1.0000. + +Reference files live in +`docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/`; the +example is listed under the **Single Crystal** section of +`docs/docs/verification/index.md` and linked from the features page +(§2.2 single-crystal Time-of-Flight row). diff --git a/docs/dev/issues/closed/reconcile-git-ignored-agents-md-claude-md-with-their-checked-in-role.md b/docs/dev/issues/closed/reconcile-git-ignored-agents-md-claude-md-with-their-checked-in-role.md index 5910302be..e85840058 100644 --- a/docs/dev/issues/closed/reconcile-git-ignored-agents-md-claude-md-with-their-checked-in-role.md +++ b/docs/dev/issues/closed/reconcile-git-ignored-agents-md-claude-md-with-their-checked-in-role.md @@ -4,9 +4,12 @@ Resolved by an explicit project-owner decision: `AGENTS.md` and `CLAUDE.md` are **intentionally git-ignored** and kept local-only, not committed repository artifacts. The `.gitignore` `# Agents` block keeps both files ignored, and a note at the top of `AGENTS.md` (plus a clause -in §Change Discipline) records that they are deliberately local-only and -that their `AGENTS_review-N.md` / `AGENTS_reply-N.md` artifacts are -likewise untracked and may be cleaned up once a review cycle closes. -This removes the earlier contradiction (the document described itself as -checked-in while being ignored) by adopting the local-only branch rather -than committing the files. +in §Change Discipline) records that they are deliberately local-only. +The `.gitignore` block ignores only `AGENTS.md` / `CLAUDE.md` themselves +— **not** their `AGENTS_review-N.md` / `AGENTS_reply-N.md` artifacts — +so those review/reply files stay visible in `git status` by design, a +deliberate reminder that they are temporary and must be cleaned up once +a review cycle closes (the agent never `git add`s them). This removes +the earlier contradiction (the document described itself as checked-in +while being ignored) by adopting the local-only branch rather than +committing the files. diff --git a/docs/dev/issues/index.md b/docs/dev/issues/index.md index a74981f68..1a7de60da 100644 --- a/docs/dev/issues/index.md +++ b/docs/dev/issues/index.md @@ -23,7 +23,6 @@ individual issue files** — not here. | 167 | [Add CrysFML `WDT` Parameter to Peak Shapes](open/highest_add-crysfml-wdt-parameter-to-peak-shapes.md) | `[priority] highest` | Performance / Engine feature | | 168 | [Decide X-ray Anomalous Scattering Table Source](open/highest_decide-x-ray-anomalous-scattering-table-source.md) | `[priority] highest` | Correctness / External backend / Verification | | 170 | [Document CrysFML X-ray Polarization as EasyDiffraction-Custom](open/highest_document-crysfml-x-ray-polarization-is-easydiffraction-custom.md) | `[priority] highest` | Correctness / External backend / Verification | -| 180 | [Nuclear-Only Reflection Filter Drops Valid Peaks (Breaks HS HRPT)](open/highest_nuclear-only-reflection-filter-drops-valid-peaks.md) | `[priority] highest` | Correctness / External backend | | 8 | [Add Explicit `create()` Signatures on Collections](open/high_add-explicit-create-signatures-on-collections.md) | `[priority] high` | API safety | | 61 | [Clarify Logger Default Reaction Mode](open/high_clarify-logger-default-reaction-mode.md) | `[priority] high` | Design | | 66 | [Decide Error-Handling Strategy: `log.error` vs `raise`](open/high_decide-error-handling-strategy-log-error-vs-raise.md) | `[priority] high` | Design | @@ -72,6 +71,9 @@ individual issue files** — not here. | 174 | [Bulk Write-Back of Calculated Intensity During Fits](open/medium_bulk-write-back-of-calculated-intensity-during-fits.md) | `[priority] medium` | Performance | | 175 | [Avoid the CIF Round-Trip on Every Public `calculate()`](open/medium_avoid-cif-round-trip-on-every-public-calculate.md) | `[priority] medium` | Performance | | 179 | [Investigate a Better Automatic `cutoff_fwhm` Detection Mechanism](open/medium_better-automatic-cutoff-fwhm-detection.md) | `[priority] medium` | Performance / Engine feature | +| 182 | [Display `engine` Setter Swallows `ValueError` and Is Off-Contract](open/medium_display-engine-setter-swallows-valueerror-and-is-off-contract.md) | `[priority] medium` | Robustness / Architecture | +| 183 | [Add Mixin Tests for TOF Size/Strain Parameters](open/medium_add-mixin-tests-for-tof-size-strain-parameters.md) | `[priority] medium` | Test coverage | +| 187 | [`fork()` in a Multi-Threaded Process (BUMPS/DREAM)](open/medium_fork-in-multi-threaded-process-deprecation-in-bumps-dream.md) | `[priority] medium` | Forward-compatibility / Concurrency | | 9 | [Add Future Enum Extensions](open/low_add-future-enum-extensions.md) | `[priority] low` | Design improvement | | 10 | [Unify Project-Level Update Orchestration](open/low_unify-project-level-update-orchestration.md) | `[priority] low` | Maintainability | | 11 | [Document Category `_update` Contract](open/low_document-category-update-contract.md) | `[priority] low` | Maintainability | @@ -153,10 +155,17 @@ individual issue files** — not here. | 159 | [Narrow Defensive getattr-Chain in Aniso ADP Unit Resolution](open/low_narrow-defensive-getattr-chain-in-aniso-adp-unit-resolution.md) | `[priority] low` | Maintainability | | 160 | [Replace No-Op `assert True` in `test_logging.py`](open/low_replace-no-op-assert-true-in-test-logging-py.md) | `[priority] low` | Test coverage | | 161 | [Add Boundary Tests for `verification.py` FullProf/IGOR Parsers](open/low_add-boundary-tests-for-verification-py-fullprof-igor-parsers.md) | `[priority] low` | Test coverage | -| 163 | [Fix `.gitignore` Gaps and Remove the Stale `absorption/` Package](open/low_fix-gitignore-gaps-and-remove-the-stale-absorption-package.md) | `[priority] low` | Hygiene | +| 163 | [Fix `.gitignore` Gaps (`.pyc` Pattern and `benchmark.json`)](open/low_fix-gitignore-pyc-and-benchmark-gaps.md) | `[priority] low` | Hygiene | | 165 | [cryspy Backend Hardcodes `flag_only_nuclear` (No Magnetic Structures)](open/low_cryspy-backend-hardcodes-flag-only-nuclear-no-magnetic-structures.md) | `[priority] low` | Engine limitation | | 176 | [Reuse Reflection Record Objects Across Fit Iterations](open/low_reuse-reflection-record-objects-across-fit-iterations.md) | `[priority] low` | Performance | | 177 | [Reduce Per-Point Data-Model Overhead in Fits](open/low_reduce-per-point-data-model-overhead-in-fits.md) | `[priority] low` | Performance | +| 180 | [Re-enable `flag_only_nuclear` Pre-Filter After Upstream cryspy Fix](open/low_re-enable-nuclear-only-pre-filter-after-cryspy-fix.md) | `[priority] low` | Correctness / External backend | +| 181 | [Add `from __future__ import annotations` to All Modules](open/low_add-from-future-annotations-to-all-modules.md) | `[priority] low` | Hygiene / Consistency | +| 184 | [Replace String-Dispatch `getattr` in `core/identity.py`](open/low_replace-string-dispatch-getattr-in-core-identity.md) | `[priority] low` | Code style | +| 185 | [Replace `**kwargs` in `Logger.print`](open/low_replace-kwargs-in-logger-print.md) | `[priority] low` | Code style | +| 186 | [Test `AdpTypeEnum.description()`](open/low_test-adptypeenum-description.md) | `[priority] low` | Test coverage | +| 188 | [Track `diffpy.Structure` Deprecation Warning](open/low_track-diffpy-structure-deprecation-warning.md) | `[priority] low` | Dependency / Deprecation | +| 189 | [Quiet Expected pytest Warnings (benchmark/xdist and BUMPS)](open/low_quiet-expected-pytest-warnings-benchmark-xdist-and-bumps.md) | `[priority] low` | Test hygiene / CI noise | | 88 | [Fix Dataset 26 Description (47 Files, Not 57)](open/lowest_fix-dataset-26-description-47-files-not-57.md) | `[priority] lowest` | Data | | 91 | [Disable TODO Comment Checks in CodeFactor PRs](open/lowest_disable-todo-comment-checks-in-codefactor-prs.md) | `[priority] lowest` | CI / Tooling | | 117 | [Live-Notebook Plotly Delivery: Loader vs Native Mimetype](open/lowest_live-notebook-plotly-delivery-loader-vs-native-mimetype.md) | `[priority] lowest` | Display / Architecture | @@ -188,3 +197,4 @@ individual issue files** — not here. | 164 | [Reconcile Git-Ignored `AGENTS.md` / `CLAUDE.md` With Their Checked-In Role](closed/reconcile-git-ignored-agents-md-claude-md-with-their-checked-in-role.md) | | 172 | [Cache Wyckoff Orbit Templates to Speed Up Refinement](closed/cache-wyckoff-orbit-templates-to-speed-up-refinement.md) | | 173 | [Avoid Rebuilding the Included-Point Mask Every Fit Iteration](closed/avoid-rebuilding-included-point-mask-every-fit-iteration.md) | +| 190 | [Add a Single-Crystal TOF Fit Verification Example](closed/add-single-crystal-tof-fit-verification-example.md) | diff --git a/docs/dev/issues/open/highest_nuclear-only-reflection-filter-drops-valid-peaks.md b/docs/dev/issues/open/highest_nuclear-only-reflection-filter-drops-valid-peaks.md deleted file mode 100644 index 89eeca1db..000000000 --- a/docs/dev/issues/open/highest_nuclear-only-reflection-filter-drops-valid-peaks.md +++ /dev/null @@ -1,65 +0,0 @@ -# 180. Nuclear-Only Reflection Filter Drops Valid Peaks (Breaks HS HRPT) - -**Priority:** `[priority] highest` - -**Type:** Correctness / External backend - -The powder calculator unconditionally sets `flag_only_nuclear = True` on -every crystal before calling cryspy -([`src/easydiffraction/analysis/calculators/cryspy.py`](../../../../src/easydiffraction/analysis/calculators/cryspy.py), -in `_calculate_powder_pattern_from_dict`). In cryspy 0.12.1 this flag -activates the reflection-extinction filter added in cryspy -[PR #48](https://github.com/ikibalin/cryspy/pull/48) -(`calc_extinction_rule_by_symmetry_elements` in -`A_functions_base/structure_factor.py`). That filter is over-aggressive: -it marks a reflection extinct if it is invariant under _any single_ -symmetry operation carrying a non-integer phase -(`extinct |= invariant & non_integer_phase`), instead of summing the -phase contributions over _all_ invariant operations and checking whether -they actually cancel. For symmetric space groups (e.g. `R -3 m`, -hexagonal setting) it removes reflections that have a **non-zero** -nuclear structure factor — real Bragg peaks disappear from the -calculated pattern. cryspy PR #48 itself notes this over-filtering for -screw-axis groups and claims a grouped-sum fix, but the shipped 0.12.1 -still uses the broken per-operation `OR`. - -**Example of broken behaviour** — the HS/HRPT tutorial -([`docs/docs/tutorials/refine-hs-hrpt`](../../../docs/tutorials/refine-hs-hrpt.py), -herbertsmithite ZnCu₃(OD)₆Cl₂, space group `R -3 m`). The calculated -pattern is missing peaks the data clearly shows (e.g. around 2θ ≈ -98.3°). The four-stage refinement then compensates with over-broad -peaks, a wrong scale, and an unphysical **negative** Zn ADP, stalling at -a poor fit. Disabling the cryspy filter restores the peaks and the fit: - -| Four-stage fit | Reduced χ² | Zn `adp_iso` | -| --------------------------------------- | ---------- | ------------ | -| As shipped (`flag_only_nuclear = True`) | **18.98** | **−1.43** | -| Filter disabled (`= False`) | **1.93** | **+0.16** | - -(Reproduced with the tutorial's own inputs; neutralising -`calc_extinction_rule_by_symmetry_elements` to return all-`False` is -enough to recover χ² ≈ 1.9 with all-positive ADPs.) The 0.18.0 release -rendered this tutorial correctly because its cryspy predated PR #48. - -**Fix:** stop force-enabling the filter in the powder path — set -`flag_only_nuclear = False` in `_calculate_powder_pattern_from_dict`, -matching the sibling `calculate_structure_factors`, which already sets -it `False` with the in-code comment _"= True fails for hs-hrpt example -with R -3 m"_. The flag only controls reflection-list filtering (not -magnetic computation), and genuine lattice-centering absences are still -removed by the separate `calc_pr3` check, so disabling it is safe and -only adds back zero-cost reflections. Also report the over-filtering -upstream to cryspy, since the root bug is in their PR #48; re-enable the -flag only once a cryspy release filters correctly. - -**Visible on:** the HS/HRPT tutorial page (`refine-hs-hrpt`); affects -any powder refinement whose space group triggers the cryspy over-filter. - -**Depends on:** an upstream cryspy fix for a correct -(non-over-filtering) `flag_only_nuclear` implementation, if the -pre-filter is ever to be re-enabled. - -**Recommended-priority note:** silent correctness failure — refinements -of symmetric space groups drop real peaks and converge to wrong -parameters (negative ADPs) with no error. Known one-line mitigation. -**Tier 1 (do first).** diff --git a/docs/dev/issues/open/highest_unify-uncertainty-floor-handling-across-bragg-pd-single-crystal-and-pdf-data.md b/docs/dev/issues/open/highest_unify-uncertainty-floor-handling-across-bragg-pd-single-crystal-and-pdf-data.md index 1f455cfa4..58817eea6 100644 --- a/docs/dev/issues/open/highest_unify-uncertainty-floor-handling-across-bragg-pd-single-crystal-and-pdf-data.md +++ b/docs/dev/issues/open/highest_unify-uncertainty-floor-handling-across-bragg-pd-single-crystal-and-pdf-data.md @@ -38,3 +38,10 @@ uncertainty). Related to issue 15 (joint-fit weights). audit: inconsistent uncertainty-floor handling yields silent NaN/inf residuals — the same residual-safety class as the Tier 1 joint-fit weight issues (#3 / #15). + +**Audit note (2026-06-23):** within Bragg PD the near-zero clamp itself +is duplicated — the CIF-read `intensity_meas_su` property and the ASCII +loader (`bragg_pd.py:163`) each apply their own +`np.where(su < _MIN_UNCERTAINTY, 1.0, …)`. Centralising the floor on +`NumericDescriptor` (the planned fix) removes this duplication too, so +CIF and ASCII inputs cannot diverge. diff --git a/docs/dev/issues/open/low_add-from-future-annotations-to-all-modules.md b/docs/dev/issues/open/low_add-from-future-annotations-to-all-modules.md new file mode 100644 index 000000000..33baec34c --- /dev/null +++ b/docs/dev/issues/open/low_add-from-future-annotations-to-all-modules.md @@ -0,0 +1,29 @@ +# 181. Add `from __future__ import annotations` to All Modules + +**Priority:** `[priority] low` + +**Type:** Hygiene / Consistency + +`AGENTS.md` (Code Style) requires `from __future__ import annotations` +in **every** module, but many source files lack it. The linter does not +enforce it universally, so the convention has drifted. + +No count is quoted here on purpose: the number is highly sensitive to +scope (whether package `__init__.py` files and vendored snapshots are +counted), and independent passes disagreed — any bare figure is +misleading without its exact command and scope. + +**Fix:** + +1. Fix the counting scope first — exclude vendored paths + (`report/templates/.../vendor/`, `report/templates/tex/styles/`, + `utils/_vendored/...`), and decide whether package `__init__.py` + files must carry the import. +2. Generate the exact list with a recorded command, e.g. + `grep -L "from __future__ import annotations" $(find src/easydiffraction -name '*.py' -not -path '*/vendor/*' -not -path '*/_vendored/*' -not -path '*/styles/*')`. +3. Add the import as the first import line of each listed module in one + mechanical pass. + +Priority is consistency, not correctness — no functional impact. + +**Depends on:** nothing. diff --git a/docs/dev/issues/open/low_clarify-cell-update-usage-of-called-by-minimizer.md b/docs/dev/issues/open/low_clarify-cell-update-usage-of-called-by-minimizer.md index e21124bfb..c27de8e3a 100644 --- a/docs/dev/issues/open/low_clarify-cell-update-usage-of-called-by-minimizer.md +++ b/docs/dev/issues/open/low_clarify-cell-update-usage-of-called-by-minimizer.md @@ -11,3 +11,10 @@ - [default.py](src/easydiffraction/datablocks/structure/categories/cell/default.py#L146) **Depends on:** related to issue 11. + +**Audit note (2026-06-23):** `Cell._update` accepts +`called_by_minimizer`, immediately `del`s it (`default.py:176-192`, +docstring "Currently unused"), yet the flag is threaded through the +whole update chain (`bragg_pd.py:786`, `total_pd.py:261`). Resolve by +either implementing the intended fast-path (skip the symmetry recompute +during fitting) or dropping the dead parameter from the chain. diff --git a/docs/dev/issues/open/low_fix-gitignore-gaps-and-remove-the-stale-absorption-package.md b/docs/dev/issues/open/low_fix-gitignore-gaps-and-remove-the-stale-absorption-package.md deleted file mode 100644 index 6ed867c11..000000000 --- a/docs/dev/issues/open/low_fix-gitignore-gaps-and-remove-the-stale-absorption-package.md +++ /dev/null @@ -1,24 +0,0 @@ -# 163. Fix `.gitignore` Gaps and Remove the Stale `absorption/` Package - -**Priority:** `[priority] low` - -**Type:** Hygiene - -Several small repository-hygiene gaps: - -- `.gitignore` line `.pyc` ignores only a file literally named `.pyc`, - not `*.pyc` (intended). `__pycache__/` covers the common case, so the - rule as written does nothing. -- The `benchmarks` pixi task writes `benchmark.json` to the repo root, - but `.gitignore` has no entry for it, so it can be staged - accidentally. -- `src/easydiffraction/datablocks/experiment/categories/absorption/` - contains **no tracked source** (only a stale `__pycache__/`); the - category has no implementation yet (see issue 119). Remove the empty - package directory until the absorption category is implemented. - -**Fix:** correct the `.pyc` pattern to `*.pyc`, add `benchmark.json`, -and delete the empty `absorption/` package. - -**Depends on:** nothing (absorption implementation tracked by issue -119). diff --git a/docs/dev/issues/open/low_fix-gitignore-pyc-and-benchmark-gaps.md b/docs/dev/issues/open/low_fix-gitignore-pyc-and-benchmark-gaps.md new file mode 100644 index 000000000..bbdf15cbd --- /dev/null +++ b/docs/dev/issues/open/low_fix-gitignore-pyc-and-benchmark-gaps.md @@ -0,0 +1,22 @@ +# 163. Fix `.gitignore` Gaps (`.pyc` Pattern and `benchmark.json`) + +**Priority:** `[priority] low` + +**Type:** Hygiene + +Two small `.gitignore` gaps: + +- `.gitignore` line `.pyc` ignores only a file literally named `.pyc`, + not `*.pyc` (intended). `__pycache__/` covers the common case, so the + rule as written does nothing. +- The `benchmarks` pixi task writes `benchmark.json` to the repo root, + but `.gitignore` has no entry for it, so it can be staged + accidentally. + +**Fix:** correct the `.pyc` pattern to `*.pyc` and add `benchmark.json`. + +**Note:** an earlier version of this issue also asked to delete the +`absorption/` package as an empty stub. That is now **obsolete** — the +package contains implemented source (`base.py`, `cylinder_hewat.py`, +`none.py`, `factory.py`) from the sample-absorption feature (issue 119), +so it must **not** be removed. diff --git a/docs/dev/issues/open/low_improve-error-handling-in-crystallography-utilities.md b/docs/dev/issues/open/low_improve-error-handling-in-crystallography-utilities.md index 199fa9374..6efbca278 100644 --- a/docs/dev/issues/open/low_improve-error-handling-in-crystallography-utilities.md +++ b/docs/dev/issues/open/low_improve-error-handling-in-crystallography-utilities.md @@ -14,3 +14,11 @@ raise `ValueError` or provide better diagnostics. - [crystallography.py](src/easydiffraction/crystallography/crystallography.py#L84) **Depends on:** nothing. + +**Audit note (2026-06-23):** concrete instance — for an unrecognised +`crystal_system`, `crystallography.py:134-138` calls `log.error(...)` +without `exc_type` and then falls through to `return cell` with no +symmetry constraints applied; under WARN logger mode this silently +returns an unconstrained cell. Fix = raise `ValueError` explicitly (and +consider modelling crystal systems as a `(str, Enum)`). Gated on the +logger-reaction decision (issues 61 / 66). diff --git a/docs/dev/issues/open/low_quiet-expected-pytest-warnings-benchmark-xdist-and-bumps.md b/docs/dev/issues/open/low_quiet-expected-pytest-warnings-benchmark-xdist-and-bumps.md new file mode 100644 index 000000000..6a09d7953 --- /dev/null +++ b/docs/dev/issues/open/low_quiet-expected-pytest-warnings-benchmark-xdist-and-bumps.md @@ -0,0 +1,34 @@ +# 189. Quiet Expected pytest Warnings (benchmark/xdist and BUMPS) + +**Priority:** `[priority] low` + +**Type:** Test hygiene / CI noise + +Two recurring, expected warnings clutter the integration-test output but +are not defects: + +- **`PytestBenchmarkWarning: Benchmarks are automatically disabled because xdist plugin is active`** + — `integration-tests` runs with `-n auto` (`pixi.toml:108`), and + `pytest-benchmark` is installed, so the plugin warns on every worker + that benchmarking is disabled. There are **no benchmarks under + `tests/integration/`**, so this is pure noise from loading the plugin + during a parallel run (benchmarks are a separate nightly concern). +- **`bumps/fitproblem.py: UserWarning: Need more data points (currently: N) than fitting parameters (N)`** + — emitted by intentionally minimal plumbing fixtures in + `tests/integration/fitting/test_bumps_dream_support.py` (`n_points=2`, + and `n_points=0` for the mapper-pickle test) and the DREAM resume + tests. The under-determined problem is deliberate (these tests + exercise mapper/pickle/resume, not a real fit), so the warning is + expected. + +Neither indicates a bug; both just make CI logs noisier and can mask new +warnings. + +**Fix:** quiet the two expected warnings at their source — e.g. disable +the `pytest-benchmark` plugin for the parallel `integration-tests` run +(`-p no:benchmark`), and add scoped `filterwarnings` entries (or +`pytest.warns`/`recwarn` assertions) for the BUMPS under-determined +warning in the specific plumbing tests — so the suite stays quiet and +any new warning stands out. + +**Depends on:** nothing. diff --git a/docs/dev/issues/open/low_re-enable-nuclear-only-pre-filter-after-cryspy-fix.md b/docs/dev/issues/open/low_re-enable-nuclear-only-pre-filter-after-cryspy-fix.md new file mode 100644 index 000000000..66ecc407f --- /dev/null +++ b/docs/dev/issues/open/low_re-enable-nuclear-only-pre-filter-after-cryspy-fix.md @@ -0,0 +1,62 @@ +# 180. Re-enable `flag_only_nuclear` Pre-Filter After Upstream cryspy Fix + +**Priority:** `[priority] low` + +**Type:** Correctness / External backend (upstream tracking + +performance) + +**Status:** The user-facing correctness symptom is **already mitigated** +in EasyDiffraction. Both the powder path and the structure-factor path +set `flag_only_nuclear = False` +([`cryspy.py:295`](../../../../src/easydiffraction/analysis/calculators/cryspy.py) +and `:187`), so the over-aggressive cryspy reflection-extinction filter +is no longer triggered and real Bragg peaks are no longer dropped. +HS/HRPT refines correctly again (reduced χ² ≈ 1.9 with all-positive +ADPs, vs χ² ≈ 19 and a negative Zn ADP when the filter was active). This +issue now tracks only the upstream bug and the eventual re-enable. + +## Background (resolved locally) + +The powder calculator used to unconditionally set +`flag_only_nuclear = True` before calling cryspy. In cryspy 0.12.1 this +activates the reflection-extinction filter from cryspy +[PR #48](https://github.com/ikibalin/cryspy/pull/48) +(`calc_extinction_rule_by_symmetry_elements` in +`A_functions_base/structure_factor.py`). That filter is over-aggressive: +it marks a reflection extinct if it is invariant under _any single_ +symmetry operation carrying a non-integer phase +(`extinct |= invariant & non_integer_phase`), instead of summing the +phase contributions over _all_ invariant operations and checking whether +they actually cancel. For symmetric space groups (e.g. `R -3 m`, +hexagonal setting — the HS/HRPT herbertsmithite tutorial) it removed +reflections with a non-zero nuclear structure factor, so real Bragg +peaks (e.g. 2θ ≈ 98.3°) disappeared and the refinement compensated with +a wrong scale and an unphysical negative Zn ADP. + +The local mitigation (set `flag_only_nuclear = False`) matches the +sibling `calculate_structure_factors`, which already carried the in-code +comment _"= True fails for hs-hrpt example with R -3 m"_. The flag only +controls reflection-list filtering (not magnetic computation), and +genuine lattice-centering absences are still removed by the separate +`calc_pr3` check, so disabling it is safe and only adds back zero-cost +reflections. + +## Remaining work + +- **Report the over-filtering upstream to cryspy.** The root bug is in + cryspy PR #48; the shipped 0.12.1 still uses the broken per-operation + `OR` rather than the grouped-sum cancellation that PR #48 itself + describes. +- **Re-enable the pre-filter once cryspy filters correctly.** Restoring + `flag_only_nuclear = True` is a performance optimization — it lets + cryspy skip computing reflections that are then discarded — so it is + worth doing only after a cryspy release filters correctly. Until then + the `False` setting is the correct behaviour. + +**Depends on:** an upstream cryspy fix for a correct +(non-over-filtering) `flag_only_nuclear` implementation. + +**Priority note:** downgraded from `highest` to `low` on 2026-06-23 — +the silent-wrong-science symptom is fixed locally (see Status); what +remains is upstream tracking plus an optional performance re-enable, +neither urgent. diff --git a/docs/dev/issues/open/low_redirect-or-suppress-cryspy-stderr-warnings.md b/docs/dev/issues/open/low_redirect-or-suppress-cryspy-stderr-warnings.md index 5c984e34c..d8bdd2207 100644 --- a/docs/dev/issues/open/low_redirect-or-suppress-cryspy-stderr-warnings.md +++ b/docs/dev/issues/open/low_redirect-or-suppress-cryspy-stderr-warnings.md @@ -4,12 +4,21 @@ **Type:** UX -CrysPy emits warnings to stderr during pattern calculation. The code has -TODO markers to redirect these. +CrysPy emits warnings to stderr during pattern calculation. -**TODOs:** +**Mostly implemented.** Both computation entry points already wrap the +cryspy call in `contextlib.redirect_stderr(io.StringIO())` +(`cryspy.py:195` and `:343`). The original TODO line references +(`#L112`, `#L184`) are stale — line 112 is now unrelated code. -- [cryspy.py](src/easydiffraction/analysis/calculators/cryspy.py#L112) -- [cryspy.py](src/easydiffraction/analysis/calculators/cryspy.py#L184) +**Remaining work:** + +- Remove the two now-satisfied + `# TODO: Redirect stderr to suppress Cryspy warnings.` comments that + still sit directly above the working redirects (`cryspy.py:190`, + `:338`). +- Confirm no other cryspy call path emits unredirected stderr (audit the + remaining cryspy entry points and extend the redirect if any are + missed). **Depends on:** nothing. diff --git a/docs/dev/issues/open/low_remove-stale-commented-out-dead-code-in-core-and-io.md b/docs/dev/issues/open/low_remove-stale-commented-out-dead-code-in-core-and-io.md index b8106435f..f757e2606 100644 --- a/docs/dev/issues/open/low_remove-stale-commented-out-dead-code-in-core-and-io.md +++ b/docs/dev/issues/open/low_remove-stale-commented-out-dead-code-in-core-and-io.md @@ -16,3 +16,10 @@ removable. - [variable.py](src/easydiffraction/core/variable.py#L167) **Depends on:** nothing. + +**Audit note (2026-06-23):** further removable blocks found beyond those +listed — a disabled `JupyterScrollManager.disable_jupyter_scroll()` call +in `display/__init__.py:15-18` (TODO "breaks MkDocs builds"), a +commented `_description` in `data/bragg_pd.py:742-744`, and a +`# TODO: Check the following methods:` marker in +`io/cif/serialize.py:860`. diff --git a/docs/dev/issues/open/low_replace-kwargs-in-logger-print.md b/docs/dev/issues/open/low_replace-kwargs-in-logger-print.md new file mode 100644 index 000000000..e40f08faa --- /dev/null +++ b/docs/dev/issues/open/low_replace-kwargs-in-logger-print.md @@ -0,0 +1,23 @@ +# 185. Replace `**kwargs` in `Logger.print` + +**Priority:** `[priority] low` + +**Type:** Code style / Convention + +`Logger.print(cls, *objects, **kwargs)` +(`src/easydiffraction/utils/logging.py:683`) forwards `**kwargs` to the +Rich console, which `AGENTS.md` (Code Style) forbids ("No `**kwargs` — +use explicit keyword arguments"). `Logger.print` is a project-owned +public façade, so it should enumerate the Rich console options it +actually supports rather than passing an open `**kwargs`. + +(Other `**kwargs` occurrences are arguable framework plumbing — +`super().__init__` chains in `core/variable.py` / factory code, or +`object`-typed minimizer-solver passthroughs to third-party libraries — +and are out of scope here.) + +**Fix:** replace `**kwargs` on `Logger.print` with the explicit keyword +arguments it forwards, or document the framework-passthrough exception +if intentional. + +**Depends on:** nothing. diff --git a/docs/dev/issues/open/low_replace-string-dispatch-getattr-in-core-identity.md b/docs/dev/issues/open/low_replace-string-dispatch-getattr-in-core-identity.md new file mode 100644 index 000000000..d78581569 --- /dev/null +++ b/docs/dev/issues/open/low_replace-string-dispatch-getattr-in-core-identity.md @@ -0,0 +1,21 @@ +# 184. Replace String-Dispatch `getattr` in `core/identity.py` + +**Priority:** `[priority] low` + +**Type:** Code style / Convention + +`Identity._resolve_up` builds attribute names by string interpolation — +`getattr(self, f'_{attr}', None)` +(`src/easydiffraction/core/identity.py:38`), where `attr` is one of +`datablock_entry` / `category_code` / `category_entry`. `AGENTS.md` +(Code Style) forbids string-based dispatch +(`getattr(self, f'_{name}')`). The value is internal (not user input), +so it plausibly fits the "narrow framework metadata lookup" exception, +but it is not validated in one central place and the three values are +not modeled as an enum — so it sits in a gray zone of the rule. + +**Fix:** replace with explicit resolver branches/methods, or model the +three allowed values as a `(str, Enum)` validated centrally, so the +lookup lands cleanly inside the documented metadata-lookup exception. + +**Depends on:** nothing. diff --git a/docs/dev/issues/open/low_test-adptypeenum-description.md b/docs/dev/issues/open/low_test-adptypeenum-description.md new file mode 100644 index 000000000..417113b86 --- /dev/null +++ b/docs/dev/issues/open/low_test-adptypeenum-description.md @@ -0,0 +1,18 @@ +# 186. Test `AdpTypeEnum.description()` + +**Priority:** `[priority] low` + +**Type:** Testing + +`AdpTypeEnum.description()` +(`src/easydiffraction/datablocks/structure/categories/atom_sites/enums.py:24`) +returns per-member human-readable text but is never exercised. The +enum's members and `.default()` are tested, but `description()` is not — +inconsistent with sibling enums (`SampleFormEnum`, +`PeakProfileTypeEnum`), which do test it. + +**Fix:** add a parametrized test (in the `test_atom_sites.py` rollup, or +a dedicated enum test) iterating `AdpTypeEnum` members and asserting +`description()` returns a non-empty `str` for each. + +**Depends on:** nothing. diff --git a/docs/dev/issues/open/low_track-diffpy-structure-deprecation-warning.md b/docs/dev/issues/open/low_track-diffpy-structure-deprecation-warning.md new file mode 100644 index 000000000..73e4399ca --- /dev/null +++ b/docs/dev/issues/open/low_track-diffpy-structure-deprecation-warning.md @@ -0,0 +1,35 @@ +# 188. Track `diffpy.Structure` Deprecation Warning + +**Priority:** `[priority] low` + +**Type:** Dependency / Deprecation + +The test suite surfaces a third-party deprecation: + +``` +DeprecationWarning: Module 'diffpy.Structure' is deprecated and will be +removed in version 4.0. Use 'diffpy.structure' instead. +``` + +EasyDiffraction's own code already uses the new lowercase module +(`from diffpy.structure.parsers.p_cif import P_cif` in +`src/easydiffraction/analysis/calculators/pdffit.py:108`), so the +deprecated capital-`S` `diffpy.Structure` is imported by a **transitive +dependency** (diffpy / `diffpy.pdffit2`) and merely surfaced when +Hypothesis scans installed modules +(`hypothesis/internal/conjecture/providers.py`). + +The risk is real but external: when diffpy 4.0 removes +`diffpy.Structure`, whatever dependency still imports it breaks. + +**Fix:** + +1. Identify which installed package imports `diffpy.Structure` + (capital). +2. If it is a pinned dependency we control, bump/track it; otherwise + record the upstream-tracking dependency and watch for the diffpy 4.0 + migration. +3. Optionally add a scoped `filterwarnings` entry so this third-party + deprecation does not clutter our test output in the meantime. + +**Depends on:** nothing (external dependency). diff --git a/docs/dev/issues/open/low_verify-completeness-of-analysis-cif-serialisation.md b/docs/dev/issues/open/low_verify-completeness-of-analysis-cif-serialisation.md index e5d19de3f..282b3ec20 100644 --- a/docs/dev/issues/open/low_verify-completeness-of-analysis-cif-serialisation.md +++ b/docs/dev/issues/open/low_verify-completeness-of-analysis-cif-serialisation.md @@ -9,4 +9,11 @@ joint-fit weights, minimiser type, calculator assignments. Any missing fields means a loaded project silently differs from the saved one. +**Priority note:** kept `low` deliberately. This is a _verification_ +task — no concrete dropped field has been identified yet. It describes +the same silent save/load-drift class as the confirmed persistence +defects (issues 139 `highest`, 142 `medium`), but unlike those it names +no reproduced loss; if the audit turns up a real missing field, split +that out as its own issue and prioritise it on its merits. + **Depends on:** related to issue 121. diff --git a/docs/dev/issues/open/medium_add-mixin-tests-for-tof-size-strain-parameters.md b/docs/dev/issues/open/medium_add-mixin-tests-for-tof-size-strain-parameters.md new file mode 100644 index 000000000..65bbc6a1e --- /dev/null +++ b/docs/dev/issues/open/medium_add-mixin-tests-for-tof-size-strain-parameters.md @@ -0,0 +1,24 @@ +# 183. Add Mixin Tests for TOF Size/Strain Parameters + +**Priority:** `[priority] medium` + +**Type:** Testing + +The microstructural size/strain feature added four `Parameter`s to the +TOF peak mixin (`broad_gauss_size_g`, `broad_gauss_strain_g`, +`broad_lorentz_size_l`, `broad_lorentz_strain_l` in +`src/easydiffraction/datablocks/experiment/categories/peak/tof_mixins.py`), +but they are never asserted at the mixin-test level. Their value +hand-off is covered indirectly via +`tests/unit/.../analysis/calculators/test_cryspy.py`, yet the public +mixin properties themselves (read returns a `Parameter`, assignment +updates the value, range validation) have no direct test — unlike every +sibling parameter in `test_tof_mixins.py`. + +**Fix:** in +`tests/unit/easydiffraction/datablocks/experiment/categories/peak/test_tof_mixins.py`, +assert that the four parameters appear in `p.parameters`, default to +`0.0`, and update via their setters (mirroring the existing σ₀/α₁ setter +checks). + +**Depends on:** nothing. diff --git a/docs/dev/issues/open/medium_bragg-powder-ascii-loader-returns-zero-points-instead-of-raising.md b/docs/dev/issues/open/medium_bragg-powder-ascii-loader-returns-zero-points-instead-of-raising.md index 94f6057ec..4975e6035 100644 --- a/docs/dev/issues/open/medium_bragg-powder-ascii-loader-returns-zero-points-instead-of-raising.md +++ b/docs/dev/issues/open/medium_bragg-powder-ascii-loader-returns-zero-points-instead-of-raising.md @@ -21,3 +21,11 @@ families. — the consistent (raising) reference **Depends on:** related to issue 66 (`log.error` vs `raise` strategy). + +**Audit note (2026-06-23):** the same loader has a second boundary bug. +`io/ascii.py:270` returns `np.loadtxt(...)`, which is **1-D** for a +single-row file, so the caller's `data.shape[1]` (`bragg_pd.py:141`) +raises an opaque `IndexError: tuple index out of range` instead of the +clear "needs ≥2 columns" message. Fix both together — normalise with +`np.atleast_2d(...)` in the loader, and raise (not `return 0`) on +too-few columns. diff --git a/docs/dev/issues/open/medium_clarify-cryspy-tof-background-cif-tag-names.md b/docs/dev/issues/open/medium_clarify-cryspy-tof-background-cif-tag-names.md index 7b492b849..1feda325e 100644 --- a/docs/dev/issues/open/medium_clarify-cryspy-tof-background-cif-tag-names.md +++ b/docs/dev/issues/open/medium_clarify-cryspy-tof-background-cif-tag-names.md @@ -17,3 +17,13 @@ mapping and the hardcoded defaults need verification. - [cryspy.py](src/easydiffraction/analysis/calculators/cryspy.py#L739) **Depends on:** nothing. + +**Audit note (2026-06-23):** `_cif_background_section` +(`cryspy.py:1718-1725`) writes, for both CWL and TOF, two background +points at `twotheta_min`/`twotheta_max` with hardcoded `0.0` intensity; +for TOF the tag is `_tof_backgroundpoint_time` but the values are 2θ, +not TOF times. This is **not** a wrong-science risk: the user's real +background is added at the model layer — `data/bragg_pd.py:578` writes +`calc + self.intensity_bkg` — so this dummy CIF section is +dead/cosmetic. Fix = remove it (or populate it correctly, with TOF times +for TOF) and drop the mislabeled tags. diff --git a/docs/dev/issues/open/medium_display-engine-setter-swallows-valueerror-and-is-off-contract.md b/docs/dev/issues/open/medium_display-engine-setter-swallows-valueerror-and-is-off-contract.md new file mode 100644 index 000000000..05e8f2ea8 --- /dev/null +++ b/docs/dev/issues/open/medium_display-engine-setter-swallows-valueerror-and-is-off-contract.md @@ -0,0 +1,28 @@ +# 182. Display `engine` Setter Swallows `ValueError` and Is Off-Contract + +**Priority:** `[priority] medium` + +**Type:** Robustness / Architecture + +Two related problems in the display renderer base +(`src/easydiffraction/display/base.py`): + +- **Swallowed boundary error.** The `engine` setter (`base.py:56-76`) + wraps the factory `create(new_engine)` in `try/except ValueError`, + logs a warning, and `return`s — silently leaving the engine unchanged + when a user passes an unsupported engine name. This is a user-input + boundary that should fail loudly (raise), not warn-and-continue. +- **Off-contract selector surface.** `RendererBase` exposes a writable + `engine` property (`:44`, `:56`) plus `show_supported_engines()` + (`:85`) and `show_current_engine()` (`:99`). This does not match the + category-owned-selector contract + ([`switchable-category-owned-selectors.md`](../../adrs/accepted/switchable-category-owned-selectors.md): + `.type`, `show_supported()`, private `_swap_*`). + +**Fix:** raise on an unsupported engine instead of +warning-and-returning; and decide whether renderer engine selection +should follow the switchable-category contract or be explicitly +documented as exempt (a display-only backend, not a domain switchable). + +**Depends on:** related to issues 61 / 66 (`log.error` vs `raise` +strategy). diff --git a/docs/dev/issues/open/medium_fork-in-multi-threaded-process-deprecation-in-bumps-dream.md b/docs/dev/issues/open/medium_fork-in-multi-threaded-process-deprecation-in-bumps-dream.md new file mode 100644 index 000000000..62ed8e481 --- /dev/null +++ b/docs/dev/issues/open/medium_fork-in-multi-threaded-process-deprecation-in-bumps-dream.md @@ -0,0 +1,41 @@ +# 187. `fork()` in a Multi-Threaded Process (BUMPS/DREAM) + +**Priority:** `[priority] medium` + +**Type:** Forward-compatibility / Concurrency + +The test suite emits, on Python 3.12+ (seen on 3.12 and 3.14): + +``` +multiprocessing/popen_fork.py: DeprecationWarning: This process is +multi-threaded, use of fork() may lead to deadlocks in the child. + self.pid = os.fork() +``` + +It fires whenever BUMPS/DREAM starts worker processes via the default +`fork` start method while the process already has live threads. Seen in: + +- unit: + `tests/unit/easydiffraction/analysis/minimizers/test_bumps_dream.py::test_run_solver_preserves_parameter_order_and_forwards_init` +- integration: + `tests/integration/fitting/test_bumps_dream_support.py::test_run_solver_preserves_parameter_order_and_forwards_init` + and the DREAM resume tests. + +This is not just log noise: Python is hardening fork-while-threaded +(slated to change the default start method), and fork in a +multi-threaded parent genuinely risks child-process deadlocks — exactly +the `MPMapper` startup path EasyDiffraction drives. + +**Tension with issue 95.** Issue 95 (Re-Enable DREAM Multiprocessing) +proposes _preferring_ a `fork` context for direct-script entry points. +That recommendation must be reconciled with this warning: the chosen +multiprocessing policy needs to be safe for fork-while-threaded (or use +`forkserver`/`spawn` with import-safe workers), not just fast. + +**Fix:** decide and document an explicit multiprocessing start-method +policy for the Bayesian backends that is safe under Python's +fork-while-threaded deprecation (e.g. `forkserver`, or `spawn` with +import-safe worker entry points), and align issue 95's solution with it. + +**Depends on:** related to issue 95 (multiprocessing start-method +policy). diff --git a/docs/dev/issues/open/medium_re-enable-dream-multiprocessing-in-direct-python-scripts.md b/docs/dev/issues/open/medium_re-enable-dream-multiprocessing-in-direct-python-scripts.md index 33a41bd67..eb78d742b 100644 --- a/docs/dev/issues/open/medium_re-enable-dream-multiprocessing-in-direct-python-scripts.md +++ b/docs/dev/issues/open/medium_re-enable-dream-multiprocessing-in-direct-python-scripts.md @@ -30,4 +30,13 @@ existing behavior for import-safe module entry points such as unavailable. Document the tradeoff clearly because `fork` on macOS is less conservative than `spawn`. -**Depends on:** related to issue 89, but independent. +**Caveat — reconcile with issue 187.** Preferring a `fork` context here +conflicts with the fork-while-threaded `DeprecationWarning` tracked in +issue 187: Python 3.12+ warns that `fork()` in a multi-threaded process +can deadlock the child, and is hardening the default start method. Any +start-method policy chosen here must be safe under that deprecation +(e.g. `forkserver`, or `spawn` with import-safe worker entry points), +not simply default to `fork`. + +**Depends on:** related to issue 89, but independent. See issue 187 for +the fork-while-threaded deprecation constraint. diff --git a/docs/dev/issues/open/medium_refactor-data-update-methods-split-and-unify.md b/docs/dev/issues/open/medium_refactor-data-update-methods-split-and-unify.md index 6f7825607..da5f661d6 100644 --- a/docs/dev/issues/open/medium_refactor-data-update-methods-split-and-unify.md +++ b/docs/dev/issues/open/medium_refactor-data-update-methods-split-and-unify.md @@ -27,3 +27,10 @@ the pattern from `bragg_sc.py`. **Recommended-priority note:** Part of the data `_update` refactor cluster (with #32 / #33): decompose `_update`. **Tier 4 (maintainability).** + +**Audit note (2026-06-23):** concrete duplication to target — the +structure-accumulation loop ("for each linked structure: fetch +calculator, add `scale * calculate_pattern`, set result") is copy-pasted +across `bragg_pd.py:781-793` and `total_pd.py:240-267` (the latter's own +TODO at `total_pd.py:252` flags the divergence). Extracting it into a +shared base-class helper is the decomposition this issue asks for. diff --git a/docs/dev/package-structure/full.md b/docs/dev/package-structure/full.md index d486c0cc9..492ef61a5 100644 --- a/docs/dev/package-structure/full.md +++ b/docs/dev/package-structure/full.md @@ -666,8 +666,6 @@ │ │ │ │ └── 🏷️ class ProjectMetadata │ │ │ └── 📄 factory.py │ │ │ └── 🏷️ class ProjectMetadataFactory -│ │ ├── 📁 publication -│ │ ├── 📁 rendering │ │ ├── 📁 rendering_plot │ │ │ ├── 📄 __init__.py │ │ │ ├── 📄 default.py @@ -727,7 +725,6 @@ │ ├── 📁 templates │ │ ├── 📁 html │ │ └── 📁 tex -│ │ └── 📁 styles │ ├── 📄 __init__.py │ ├── 📄 data_context.py │ │ └── 🏷️ class ReportDataContext diff --git a/docs/dev/package-structure/short.md b/docs/dev/package-structure/short.md index 1e9ac8eba..13525dcc8 100644 --- a/docs/dev/package-structure/short.md +++ b/docs/dev/package-structure/short.md @@ -319,8 +319,6 @@ │ │ │ ├── 📄 __init__.py │ │ │ ├── 📄 default.py │ │ │ └── 📄 factory.py -│ │ ├── 📁 publication -│ │ ├── 📁 rendering │ │ ├── 📁 rendering_plot │ │ │ ├── 📄 __init__.py │ │ │ ├── 📄 default.py @@ -359,7 +357,6 @@ │ ├── 📁 templates │ │ ├── 📁 html │ │ └── 📁 tex -│ │ └── 📁 styles │ ├── 📄 __init__.py │ ├── 📄 data_context.py │ ├── 📄 enums.py diff --git a/docs/dev/pycrysfml-verification-feature-requests.md b/docs/dev/pycrysfml-verification-feature-requests.md new file mode 100644 index 000000000..f7173c196 --- /dev/null +++ b/docs/dev/pycrysfml-verification-feature-requests.md @@ -0,0 +1,100 @@ +# pycrysfml feature requests from verification examples + +Feature requests to open as individual issues in +`https://github.com/easyscience/deps-pycrysfml/issues`. + +Each request below maps to one EasyDiffraction FullProf verification +example and asks for **one main feature** so that pycrysfml can +reproduce that example's calculated powder pattern. For every request, +the only files attached to the issue are the FullProf **`.pcr`** (model +and instrument definition) and **`.dat`** (measured data) — they are +attached purely as a reference for what the feature should produce, not +as files pycrysfml is expected to read. + +Source examples live under `docs/docs/verification/fullprof//`. + +--- + +## Request 1: TOF Jorgensen profile for neutron powder patterns + +**Short description:** + +Add time-of-flight (TOF) neutron powder-pattern calculation using the +**Jorgensen** peak shape — back-to-back exponentials convoluted with a +Gaussian (FullProf `NPROF=9` with the Lorentzian component switched off, +`Gamma=0`). The example is a constant-time-step TOF Si pattern on the +backscattering bank (`2theta=144.845`), with the peak shape supplied +through a numerical TOF IRF look-up table (`D2TOF`, `Sigma`, `Alpha`, +`Beta`). pycrysfml should map TOF d-spacing to time-of-flight via the +`Dtt1`/`Dtt2`/`Zero` calibration and return the calculated intensity. + +- Example: `pd-neut-tof_si_jorgensen` +- Reference files: `arg_si.pcr`, `arg_si.dat` + +--- + +## Request 2: TOF Jorgensen-Von Dreele profile for neutron powder patterns + +**Short description:** + +Add the **Jorgensen-Von Dreele** TOF peak shape — back-to-back +exponentials convoluted with a full **pseudo-Voigt** (FullProf `NPROF=9` +with a non-zero Lorentzian component, `Gamma>0`). This extends Request 1 +with the Lorentzian broadening term so that pycrysfml can select between +the pure-Gaussian Jorgensen profile and the Gaussian+Lorentzian Von +Dreele profile for the same Si TOF backscattering pattern. + +- Example: `pd-neut-tof_si_jorgensen-von-dreele` +- Reference files: `arg_si.pcr`, `arg_si.dat` + +--- + +## Request 3: TOF size/strain broadening parameters + +**Short description:** + +Expose the d-dependent **size and strain broadening** terms of the TOF +peak shape: the Gaussian `Sigma-1`/`Sigma-2` and Lorentzian +`Gamma-1`/`Gamma-2` coefficients (FullProf TOF profile parameters). This +example is identical to the Jorgensen-Von Dreele Si pattern but with +non-zero `Sigma-2` and `Gamma-2`, which widen the peaks through +microstructural (size/strain) broadening. pycrysfml should accept these +coefficients and apply the corresponding d-dependent peak widths. + +- Example: `pd-neut-tof_si_jorgensen-von-dreele-size-strain` +- Reference files: `arg_si.pcr`, `arg_si.dat` + +--- + +## Request 4: March-Dollase preferred orientation in CW powder patterns + +**Short description:** + +Add **March-Dollase preferred-orientation** correction to constant- +wavelength neutron powder patterns. The example is La0.5Ba0.5CoO3 (cubic +`P m -3 m`) with FullProf preferred orientation enabled (`Nor=1`, +`Pref1=1.2`, `Pref2=0.3`). pycrysfml should accept the preferred- +orientation model, the March-Dollase value (`Pref1`), and the random +fraction (`Pref2`) and apply the resulting per-reflection intensity +correction. + +- Example: `pd-neut-cwl_lbco_preferred-orientation` +- Reference files: `lbco.pcr`, `lbco.dat` + +--- + +## Request 5: X-ray constant-wavelength powder patterns + +**Short description:** + +Add **X-ray constant-wavelength** powder-pattern calculation, including +the Cu Kα **two-wavelength doublet** (`Lambda1=1.54056`, +`Lambda2=1.5444`, `Ratio=0.5`) and X-ray Lorentz-polarization. The +example is LiF (`F m -3 m`) measured with a Cu Kα doublet. pycrysfml +should use X-ray scattering factors and the X-ray Lorentz-polarization +factor, and superimpose the two wavelength components at the correct +intensity ratio. + +- Example: `pd-xray-cwl_lif` +- Reference files: `lif_doublet_unpolarized.pcr`, + `lif_doublet_unpolarized.dat` diff --git a/docs/docs/features/index.md b/docs/docs/features/index.md index 1e2d68ef1..d405cfa3e 100644 --- a/docs/docs/features/index.md +++ b/docs/docs/features/index.md @@ -97,11 +97,11 @@ The status icons:
-| Feature | LIB | CLI | APP | -| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ------------------ | ------------------ | -| Hermann-Mauguin space-group symbol
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Space group IT number
- :date: `easydiffraction` | :date: | :date: | :date: | -| IT coordinate system code
- :white_check_mark: `cryspy`
- :material-help-circle: `crysfml`
- :material-cancel: `pdffit2`
- :material-link-variant: `FullProf` ":1" (origin choice) | :ballot_box_with_check: | :white_check_mark: | :white_check_mark: | +| Feature | LIB | CLI | APP | +| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ------------------ | +| Hermann-Mauguin space-group symbol
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Space group IT number
- :date: `easydiffraction` | :date: | :date: | :date: | +| IT coordinate system code
- :white_check_mark: `cryspy`
- :material-help-circle: `crysfml`
- :material-cancel: `pdffit2`
- :material-link-variant: `FullProf` ":1" (origin choice) | :ballot_box_with_check: | :ballot_box_with_check: | :white_check_mark: |
@@ -120,15 +120,15 @@ The status icons:
-| Feature | LIB | CLI | APP | -| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ------------------ | ------------------ | -| X-ray scattering factors (tabulated)
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Neutron scattering lengths for natural elements (tabulated)
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Isotope-specific neutron scattering length _(e.g. ¹¹B, ²H)_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_11B.ipynb)
- :material-help-circle: `crysfml`
- :material-help-circle: `pdffit2` | :ballot_box_with_check: | :white_check_mark: | :date: | -| Custom neutron scattering length
- :material-cancel: `cryspy`
- :material-help-circle: `crysfml`
- :material-help-circle: `pdffit2`
- :material-link-variant: `FullProf` "Nsc (user-defined scattering)" | :date: | :date: | :date: | -| Fractional coordinates _x, y, z_
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Occupancy
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Symmetry _wyckoff_letter_
- :white_check_mark: `easydiffraction` | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Feature | LIB | CLI | APP | +| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ------------------ | +| X-ray scattering factors (tabulated)
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Neutron scattering lengths for natural elements (tabulated)
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Isotope-specific neutron scattering length _(e.g. ¹¹B, ²H)_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_11B.ipynb)
- :material-help-circle: `crysfml`
- :material-help-circle: `pdffit2` | :ballot_box_with_check: | :ballot_box_with_check: | :date: | +| Custom neutron scattering length
- :material-cancel: `cryspy`
- :material-help-circle: `crysfml`
- :material-help-circle: `pdffit2`
- :material-link-variant: `FullProf` "Nsc (user-defined scattering)" | :date: | :date: | :date: | +| Fractional coordinates _x, y, z_
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Occupancy
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Symmetry _wyckoff_letter_
- :white_check_mark: `easydiffraction` | :white_check_mark: | :white_check_mark: | :white_check_mark: |
@@ -136,21 +136,25 @@ The status icons:
-| Feature | LIB | CLI | APP | -| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ------------------ | ------------------ | -| Isotropic _Biso_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_Y2O3_isotropic-adp.ipynb)
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :date: | -| Isotropic _Uiso_
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Anisotropic _Bani_ (_B11…B23_)
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :white_check_mark: `pdffit2` | :ballot_box_with_check: | :white_check_mark: | :date: | -| Anisotropic _Uani_ (_U11…U23_)
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :white_check_mark: `pdffit2` | :ballot_box_with_check: | :white_check_mark: | :date: | -| Anisotropic _β_ (_β11…β23_)
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_Y2O3_beta-adp.ipynb)
- :date: `crysfml`
- :date: `pdffit2` | :ballot_box_with_check: | :white_check_mark: | :date: | +| Feature | LIB | CLI | APP | +| -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ------------------ | +| Isotropic _Biso_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_Y2O3_isotropic-adp.ipynb)
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2`
- :white_check_mark: `easydiffraction` (B/U/β conversion) | :white_check_mark: | :white_check_mark: | :date: | +| Isotropic _Uiso_
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2`
- :white_check_mark: `easydiffraction` (B/U/β conversion) | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Anisotropic _Bani_ (_B11…B23_)
- :white_check_mark: `cryspy`
- :material-help-circle: `crysfml`
- :white_check_mark: `pdffit2`
- :white_check_mark: `easydiffraction` (B/U/β conversion) | :ballot_box_with_check: | :ballot_box_with_check: | :date: | +| Anisotropic _Uani_ (_U11…U23_)
- :white_check_mark: `cryspy`
- :material-help-circle: `crysfml`
- :white_check_mark: `pdffit2`
- :white_check_mark: `easydiffraction` (B/U/β conversion) | :ballot_box_with_check: | :ballot_box_with_check: | :date: | +| Anisotropic _β_ (_β11…β23_)
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_Y2O3_beta-adp.ipynb)
- :material-help-circle: `crysfml`
- :material-help-circle: `pdffit2`
- :white_check_mark: `easydiffraction` (B/U/β conversion) | :ballot_box_with_check: | :ballot_box_with_check: | :date: |
!!! note CrysFML refines only isotropic ADPs today; for anisotropic atoms it - uses the isotropic-equivalent _B_, hence the :date: for `crysfml` on - the anisotropic rows. + uses the isotropic-equivalent _B_, so true anisotropic refinement in + `crysfml` is unconfirmed (:material-help-circle: on the anisotropic + rows). EasyDiffraction stores ADPs type-neutrally and converts + between _B_, _U_, and _β_ for each engine, so the `easydiffraction` + line marks that conversion. `pdffit2` works in _U_; its _β_ support + is likewise unconfirmed. --- @@ -245,9 +249,9 @@ calculated pattern; the engine is not involved.
-| Feature | LIB | CLI | APP | -| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ------------------ | ------ | -| March–Dollase: _march_r, random fraction, hkl axis_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LBCO_preferred-orientation.ipynb)
- :construction: `crysfml`
- :material-link-variant: `FullProf` "Nor=1", "Pref1/2, Pr1/2/3" | :ballot_box_with_check: | :white_check_mark: | :date: | +| Feature | LIB | CLI | APP | +| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ------ | +| March–Dollase: _march_r, random fraction, hkl axis_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LBCO_preferred-orientation.ipynb)
- :construction: `crysfml`
- :material-link-variant: `FullProf` "Nor=1", "Pref1/2, Pr1/2/3" | :ballot_box_with_check: | :ballot_box_with_check: | :date: |
@@ -260,7 +264,7 @@ calculated pattern; the engine is not involved. | Wavelength: _λ_
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :material-link-variant: `FullProf` "Lambda1" | :white_check_mark: | :white_check_mark: | :white_check_mark: | | Second wavelength: _λ₂, I₂/I₁ ratio_
- :white_check_mark: `easydiffraction` (Kα₁/Kα₂ doublet; engine run twice) [:material-check-decagram:](../verification/pd-xray-cwl_LiF_doublet.ipynb)
- :material-cancel: `cryspy`
- :construction: `crysfml`
- :material-link-variant: `FullProf` "Lambda2, Ratio" | :ballot_box_with_check: | :ballot_box_with_check: | :date: | | 2θ offset
- :white_check_mark: `easydiffraction`
- :material-link-variant: `FullProf` "Zero" | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Sample displacement and transparency corrections
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_sycos-sysin.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "SyCos, SySin" | :ballot_box_with_check: | :white_check_mark: | :date: | +| Sample displacement and transparency corrections
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_sycos-sysin.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "SyCos, SySin" | :ballot_box_with_check: | :ballot_box_with_check: | :date: | | Absorption correction (cylinder, Hewat)
- :white_check_mark: `easydiffraction` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_absorption.ipynb)
- :material-link-variant: `FullProf` "muR" | :white_check_mark: | :white_check_mark: | :date: | | X-ray Lorentz-polarization correction: _polarization coefficient, monochromator 2θ_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-xray-cwl_LiF_single_polarization.ipynb)
- :white_check_mark: `easydiffraction` (for `crysfml`)
- :material-link-variant: `FullProf` "Cthm, Rpolarz" | :white_check_mark: | :white_check_mark: | :date: | @@ -270,10 +274,10 @@ calculated pattern; the engine is not involved.
-| Feature | LIB | CLI | APP | -| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ------------------ | ------------------ | -| 2θ bank
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "2-theta bank" | :ballot_box_with_check: | :white_check_mark: | :white_check_mark: | -| d → TOF conversion: _offset, linear, quadratic (reciprocal defined but not yet wired)_
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "Zero, Dtt1, Dtt2, Dtt_1overd" | :ballot_box_with_check: | :white_check_mark: | :white_check_mark: | +| Feature | LIB | CLI | APP | +| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ------------------ | +| 2θ bank
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "2-theta bank" | :ballot_box_with_check: | :ballot_box_with_check: | :white_check_mark: | +| d → TOF conversion: _offset, linear, quadratic (reciprocal defined but not yet wired)_
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "Zero, Dtt1, Dtt2, Dtt_1overd" | :ballot_box_with_check: | :ballot_box_with_check: | :white_check_mark: |
@@ -290,9 +294,9 @@ and time-of-flight modes.
-| Feature | LIB | CLI | APP | -| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ------------------ | ------ | -| Peak-range cutoff (speed vs accuracy)
_cutoff in FWHMs; 0 = full range_
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "WDT" | :ballot_box_with_check: | :white_check_mark: | :date: | +| Feature | LIB | CLI | APP | +| ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ------ | +| Peak-range cutoff (speed vs accuracy)
_cutoff in FWHMs; 0 = full range_
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "WDT" | :ballot_box_with_check: | :ballot_box_with_check: | :date: |
@@ -300,11 +304,11 @@ and time-of-flight modes.
-| Feature | LIB | CLI | APP | -| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ------------------ | ------------------ | -| Thompson-Cox-Hastings pseudo-Voigt
_Gaussian U, V, W
Lorentzian X, Y_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_basic.ipynb)
- :white_check_mark: `crysfml` [:material-check-decagram:](../verification/pd-xray-cwl_LiF_single.ipynb)
- :material-link-variant: `FullProf` "Npr=7" | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Thompson-Cox-Hastings pseudo-Voigt + Bérar-Baldinozzi asymmetry
_Gaussian U, V, W
Lorentzian X, Y_
_Bérar-Baldinozzi asymmetry a₀, b₀, a₁, b₁_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_PbSO4_beba-asymmetry.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=7" + "Asy1-4" | :ballot_box_with_check: | :white_check_mark: | :white_check_mark: | -| Thompson-Cox-Hastings pseudo-Voigt + Finger-Cox-Jephcoat asymmetry
_Gaussian U, V, W
Lorentzian X, Y_
_Finger-Cox-Jephcoat asymmetry 1, 2_
- :material-cancel: `cryspy`
- :white_check_mark: `crysfml` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_fcj-asymmetry.ipynb)
- :material-link-variant: `FullProf` "Npr=7" + "S_L/D_L" | :white_check_mark: | :white_check_mark: | :date: | +| Feature | LIB | CLI | APP | +| ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------ | ------------------ | ------------------ | +| Thompson-Cox-Hastings pseudo-Voigt
_Gaussian broadening U, V, W
Lorentzian broadening X, Y_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_basic.ipynb)
- :white_check_mark: `crysfml` [:material-check-decagram:](../verification/pd-xray-cwl_LiF_single.ipynb)
- :material-link-variant: `FullProf` "Npr=7" | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Thompson-Cox-Hastings pseudo-Voigt + Bérar-Baldinozzi asymmetry
_Gaussian broadening U, V, W
Lorentzian broadening X, Y_
_Bérar-Baldinozzi asymmetry a₀, b₀, a₁, b₁_
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/pd-neut-cwl_PbSO4_beba-asymmetry.ipynb)
- :material-cancel: `crysfml`
- :material-link-variant: `FullProf` "Npr=7" + "Asy1-4" | :white_check_mark: | :white_check_mark: | :white_check_mark: | +| Thompson-Cox-Hastings pseudo-Voigt + Finger-Cox-Jephcoat asymmetry
_Gaussian broadening U, V, W
Lorentzian broadening X, Y_
_Finger-Cox-Jephcoat asymmetry 1, 2_
- :material-cancel: `cryspy`
- :white_check_mark: `crysfml` [:material-check-decagram:](../verification/pd-neut-cwl_LaB6_fcj-asymmetry.ipynb)
- :material-link-variant: `FullProf` "Npr=7" + "S_L/D_L" | :white_check_mark: | :white_check_mark: | :date: |
@@ -312,13 +316,13 @@ and time-of-flight modes.
-| Feature | LIB | CLI | APP | -| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------- | ------------------ | ------------------ | -| Pseudo-Voigt (non-convoluted)
_Gaussian σ₀, σ₁, σ₂, size_g, strain_g
Lorentzian γ₀, γ₁, γ₂, size_l, strain_l_
- :white_check_mark: `cryspy` "non-conv-pseudo-Voigt" [:material-check-decagram:](../verification/pd-neut-tof_Fe_pseudo-voigt.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=7" (TOF) | :ballot_box_with_check: | :white_check_mark: | :date: | -| Jorgensen (back-to-back exp ⊗ Gaussian)
_Gaussian σ₀, σ₁, σ₂, size_g, strain_g
Asymmetry rise α₀, α₁; decay β₀, β₁_
- :white_check_mark: `cryspy` "Gauss" [:material-check-decagram:](../verification/pd-neut-tof_Si_jorgensen.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=9" (Gaussian limit) | :ballot_box_with_check: | :white_check_mark: | :white_check_mark: | -| Jorgensen-Von Dreele (back-to-back exp ⊗ pseudo-Voigt)
_Gaussian σ₀, σ₁, σ₂, size_g, strain_g
Lorentzian γ₀, γ₁, γ₂, size_l, strain_l
Asymmetry rise α₀, α₁; decay β₀, β₁_
- :white_check_mark: `cryspy` "pseudo-Voigt" [:material-check-decagram:](../verification/pd-neut-tof_Si_jorgensen-von-dreele.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=9"; "Iso-GSize, Iso-GStrain, Iso-LorSize, Iso-LorStrain" | :ballot_box_with_check: | :white_check_mark: | :white_check_mark: | -| Double back-to-back exp ⊗ pseudo-Voigt
_Gaussian σ₀, σ₁, σ₂, size_g, strain_g
Lorentzian γ₀, γ₁, γ₂, size_l, strain_l
Asymmetry rise α₁, α₂; fast decay β₀₀, β₀₁; slow decay β₁₀; switching r₀₁, r₀₂, r₀₃_
- :white_check_mark: `cryspy` "type0m"
- :material-link-variant: Z-Rietveld "type0m" (no direct `FullProf` Npr; cf. Npr=10) | :white_check_mark: | :white_check_mark: | :date: | -| Ikeda-Carpenter ⊗ pseudo-Voigt
_Gaussian σ₀, σ₁, σ₂
Lorentzian γ₀, γ₁, γ₂
Moderator pulse α₀, α₁, β₀, κ_
- :date: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=13" | :date: | :date: | :date: | +| Feature | LIB | CLI | APP | +| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ------------------ | +| Pseudo-Voigt (non-convoluted)
_Gaussian σ₀, σ₁, σ₂, size_g, strain_g
Lorentzian broadening γ₀, γ₁, γ₂, size_l, strain_l_
- :white_check_mark: `cryspy` "non-conv-pseudo-Voigt" [:material-check-decagram:](../verification/pd-neut-tof_Fe_pseudo-voigt.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=7" (TOF) | :ballot_box_with_check: | :ballot_box_with_check: | :date: | +| Jorgensen (back-to-back exp ⊗ Gaussian)
_Gaussian broadening σ₀, σ₁, σ₂, size_g, strain_g
Asymmetry rise α₀, α₁; decay β₀, β₁_
- :white_check_mark: `cryspy` "Gauss" [:material-check-decagram:](../verification/pd-neut-tof_Si_jorgensen.ipynb)
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=9" (Gaussian limit) | :ballot_box_with_check: | :ballot_box_with_check: | :white_check_mark: | +| Jorgensen-Von Dreele (back-to-back exp ⊗ pseudo-Voigt)
_Gaussian broadening σ₀, σ₁, σ₂, size_g, strain_g
Lorentzian broadening γ₀, γ₁, γ₂, size_l, strain_l
Asymmetry rise α₀, α₁; decay β₀, β₁_
- :white_check_mark: `cryspy` "pseudo-Voigt" [:material-check-decagram:](../verification/pd-neut-tof_Si_jorgensen-von-dreele.ipynb) (size/strain [:material-check-decagram:](../verification/pd-neut-tof_Si_jorgensen-von-dreele-size-strain.ipynb))
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=9"; "Iso-GSize, Iso-GStrain, Iso-LorSize, Iso-LorStrain" | :ballot_box_with_check: | :ballot_box_with_check: | :white_check_mark: | +| Double back-to-back exp ⊗ pseudo-Voigt
_Gaussian broadening σ₀, σ₁, σ₂, size_g, strain_g
Lorentzian broadening γ₀, γ₁, γ₂, size_l, strain_l
Asymmetry rise α₁, α₂; fast decay β₀₀, β₀₁; slow decay β₁₀; switching r₀₁, r₀₂, r₀₃_
- :white_check_mark: `cryspy` "type0m"
- :material-link-variant: Z-Rietveld "type0m" (no direct `FullProf` Npr; cf. Npr=10) | :white_check_mark: | :white_check_mark: | :date: | +| Ikeda-Carpenter ⊗ pseudo-Voigt
_Gaussian broadening σ₀, σ₁, σ₂
Lorentzian broadening γ₀, γ₁, γ₂
Moderator pulse α₀, α₁, β₀, κ_
- :date: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "Npr=13" | :date: | :date: | :date: |
@@ -355,9 +359,9 @@ a Gaussian or Lorentzian mosaicity distribution.
-| Feature | LIB | CLI | APP | -| ---------------------------------------------------------------- | ------ | ------ | ------ | -| Structural twinning
- :date: `cryspy`
- :date: `crysfml` | :date: | :date: | :date: | +| Feature | LIB | CLI | APP | +| -------------------------------------------------------------------------------- | ------ | ------ | ------ | +| Structural twinning
- :date: `cryspy`
- :material-help-circle: `crysfml` | :date: | :date: | :date: |
@@ -365,10 +369,10 @@ a Gaussian or Lorentzian mosaicity distribution.
-| Feature | LIB | CLI | APP | -| ------------------------------------------------------------------------------------------------- | ------------------ | ------------------ | ------------------ | -| Wavelength
- :white_check_mark: `cryspy`
- :material-link-variant: `FullProf` "Lambda1" | :white_check_mark: | :white_check_mark: | :white_check_mark: | -| Half wavelength (λ/2)
- :date: `cryspy`
- :material-link-variant: `FullProf` "x-Lambda/2" | :date: | :date: | :date: | +| Feature | LIB | CLI | APP | +| ------------------------------------------------------------------------------------------------------------------------ | ----------------------- | ----------------------- | ------------------ | +| Wavelength
- :white_check_mark: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "Lambda1" | :ballot_box_with_check: | :ballot_box_with_check: | :white_check_mark: | +| Half wavelength (λ/2)
- :date: `cryspy`
- :date: `crysfml`
- :material-link-variant: `FullProf` "x-Lambda/2" | :date: | :date: | :date: |
@@ -376,9 +380,9 @@ a Gaussian or Lorentzian mosaicity distribution.
-| Feature | LIB | CLI | APP | -| ---------------------------------------------------------------------- | ------------------ | ------------------ | ------ | -| Individual wavelength per reflection
- :white_check_mark: `cryspy` | :white_check_mark: | :white_check_mark: | :date: | +| Feature | LIB | CLI | APP | +| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------- | ----------------------- | ------ | +| Individual wavelength per reflection
- :white_check_mark: `cryspy` [:material-check-decagram:](../verification/sc-neut-tof_taurine_basic.ipynb)
- :material-help-circle: `crysfml` | :ballot_box_with_check: | :ballot_box_with_check: | :date: |
@@ -389,6 +393,8 @@ a Gaussian or Lorentzian mosaicity distribution. Polarized-neutron powder diffraction is an epic. Planned: flipping-ratio method. +--- + ### 2.4. Polarized Single-Crystal Diffraction Polarized-neutron single-crystal diffraction is an epic. Planned: @@ -420,7 +426,7 @@ polarimetry. | -------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------- | ----------------------- | ----------------------- | | Calculate diffraction pattern (for fitting/comparison)
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :white_check_mark: `pdffit2` | :white_check_mark: | :white_check_mark: | :white_check_mark: | | Calculate diffraction pattern (simple view, no data)
- :white_check_mark: `cryspy`
- :white_check_mark: `crysfml`
- :date: `pdffit2` | :ballot_box_with_check: | :ballot_box_with_check: | :ballot_box_with_check: | -| Calculate structure factors
- :white_check_mark: `cryspy`
- :date: `crysfml` | :ballot_box_with_check: | :white_check_mark: | :white_check_mark: | +| Calculate structure factors
- :white_check_mark: `cryspy`
- :date: `crysfml` | :ballot_box_with_check: | :ballot_box_with_check: | :white_check_mark: | diff --git a/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.bac b/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.bac new file mode 100644 index 000000000..fd60097d7 --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.bac @@ -0,0 +1,1996 @@ +! 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b/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.pcr @@ -0,0 +1,66 @@ +COMM Diamond - DREAM (ESS) McStas-simulated reduced TOF data +! Current global Chi2 (Bragg contrib.) = 18.14 +! Files => DAT-file: diamond.dat, PCR-file: diamond +!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut + -1 9 1 8 2 0 0 0 0 0 0 0 0 0 0 1 0 0 1 +! +!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana + 0 2 1 0 1 0 4 0 0 2 10 1 0 0 0 0 0 +! +! Bkpos Wdt Iabscor for Pattern# 1 + 150.000 30.00 0 +!NCY Eps R_at R_an R_pr R_gl TOF-min TOF-max +100 0.05 0.01 0.01 0.01 0.01 8675.1074 29.0146 66503.6875 +! +!2Theta/TOF/E(Kev) Background for Pattern# 1 + 10000.0000 -0.2284 71.00 + 14000.0000 0.3915 81.00 + 21000.0000 0.6957 91.00 + 27500.0000 0.5692 101.00 + 40000.0000 0.3028 111.00 + 50000.0000 0.6136 121.00 + 61000.0000 0.7375 131.00 + 70000.0000 0.6141 141.00 +! +! Excluded regions (LowT HighT) for Pattern# 1 + 0.00 9999.00 + 70001.00 200000.00 +! +! + 15 !Number of refined parameters +! +! Zero Code Dtt1 Code Dtt2 Code Dtt_1overd Code 2ThetaBank -> Patt# 1 + 0.00000 0.00 28385.86133 61.00 0.00000 0.00 0.00000 0.00 90.000 +!------------------------------------------------------------------------------- +! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 16.4439 +!------------------------------------------------------------------------------- +Diamond +! +!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More + 1 0 0 0.0 0.0 1.0 0 0 0 0 0 27673.344 0 9 0 +! +! +F d -3 m:1 <--Space group symbol +!Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes +C C 0.12500 0.12500 0.12500 0.89263 1.00000 0 0 0 0 + 0.00 0.00 0.00 151.00 0.00 +!-------> Profile Parameters for Pattern # 1 ----> Phase # 1 +! Scale Extinc Bov Str1 Str2 Str3 Strain-Mode + 0.1011780 0.0000 0.0000 0.0000 0.0000 0.0000 0 + 51.00000 0.00 0.00 0.00 0.00 0.00 +! Sigma-2 Sigma-1 Sigma-0 Sigma-Q Iso-GStrain Iso-GSize Ani-LSize Size-Model + 0.0000 4887.9180 46937.7188 0.0000 0.0000 0.0000 0.0000 0 + 0.00 41.00 31.00 0.00 0.00 0.00 0.00 +! Gamma-2 Gamma-1 Gamma-0 Iso-LorStrain Iso-LorSize + 0.0000 0.0000 0.0000 0.0000 0.0000 + 0.00 0.00 0.00 0.00 0.00 +! a b c alpha beta gamma # Cell Info + 3.567000 3.567000 3.567000 90.000000 90.000000 90.000000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +! Pref1 Pref2 alph0 beta0 alph1 beta1 alphQ betaQ + 0.000000 0.000000 0.000000 0.014330 0.022544 0.000000 0.000000 0.000000 + 0.00 0.00 0.00 11.00 21.00 0.00 0.00 0.00 +!Absorption correction parameters + 0.00000 0.00 0.00000 0.00 ABS: ABSCOR1 ABSCOR2 +! 2Th1/TOF1 2Th2/TOF2 Pattern to plot + 10000.000 66503.688 1 diff --git a/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.prf b/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.prf new file mode 100644 index 000000000..e7cfb23a0 --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.prf @@ -0,0 +1,2099 @@ +IGOR +WAVES TOF, Iobs, Icalc, Diff +BEGIN + 8675.107 0.00 0.00 0.00 + 8704.108 0.33 0.00 0.33 + 8733.110 0.12 0.00 0.12 + 8762.111 0.10 0.00 0.10 + 8791.112 0.00 0.00 0.00 + 8820.114 0.44 0.00 0.44 + 8849.115 0.25 0.00 0.25 + 8878.116 0.81 0.00 0.81 + 8907.118 0.05 0.00 0.05 + 8936.119 0.00 0.00 0.00 + 8965.120 0.00 0.00 0.00 + 8994.122 0.00 0.00 0.00 + 9023.123 0.00 0.00 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-1 + 10793.537 -1 + 11047.537 -1 + 11113.890 -1 + 11113.890 -1 + 11320.358 -1 + 11614.441 -1 + 11691.614 -1 + 11691.615 -1 + 11932.704 -1 + 11932.704 -1 + 12278.650 -1 + 12369.943 -1 + 12656.545 -1 + 13181.932 -1 + 13181.932 -1 + 13530.415 -1 + 14178.164 -1 + 14178.166 -1 + 14614.518 -1 + 15264.366 -1 + 15440.839 -1 + 16009.403 -1 + 16875.393 -1 + 17114.771 -1 + 17899.057 -1 + 19486.023 -1 + 19486.023 -1 + 20668.051 -1 + 23228.883 -1 + 25313.090 -1 + 29229.035 -1 + 30528.732 -1 + 35798.113 -1 + 58458.070 -1 +END +WAVES Excrg1, excl1 +BEGIN + 8675.11 -1 + 9999.00 -1 +END +WAVES Excrg2, excl2 +BEGIN + 70001.00 -1 + 66503.69 -1 +END +X Silent 1 +X DefaultFont Times +X Display Iobs, Icalc, Diff vs TOF +X Modify mode(Iobs)=2, rgb(Iobs)=(0,0,0), rgb(Diff)=(3800,44400,4000) +X SetAxis bottom 8675.11, 66503.69 +X Modify lsize(Iobs)=2 +X Modify offset(Diff)={0, -7} +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: diamond\rDate of fit: \Z09 24/06/2026/ 12:52:13.1\Z12\rDiamond\rChi2 = 18.14" +X Label left "\Z14Intensity" +X Label bottom "\Z14 TOF(in micro-seconds)" +X TileWindows/O=1/C +X ShowInfo +X | Title of data set: Diamond - DREAM (ESS) McStas-simulated reduced TOF data +X | Date of run: 24/06/2026 / 12:52:13.1 +X Beep +X Beep diff --git a/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.sum b/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.sum new file mode 100644 index 000000000..0f05c568a --- /dev/null +++ b/docs/docs/verification/fullprof/pd-neut-tof_diamond_dream/diamond.sum @@ -0,0 +1,165 @@ + + + ********************************************************** + ** 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: 24/06/2026 Time: 12:52:10.863 + + => PCR file code: diamond + => DAT file code: diamond -> Relative contribution: 1.0000 + => Title: Diamond - DREAM (ESS) McStas-simulated reduced TOF data + + ==> CONDITIONS OF THIS RUN FOR PATTERN No.: 1 + + => Global Refinement of neutron powder data + => Neutron Time-Of-Flight data + => Abcisa variable is T.O.F. in microsecs + => The 9th default profile function was selected + + => X-Y type of data: 2theta/TOF/E(Kev) Intens sigma for pattern: 1 + => Absorption correction type: 0 + => Base of peaks: 2.0*HW* 30.00 + ==> T.O.F. range, and number of points: + TOFmin: 8675.107422 TOFmax: 66503.687500 + No. of points: 1995 + =>-------> Pattern# 1 + => Crystal Structure Refinement for phase: 1 + => The density (volumic mass) of phase 1 is: 7.032 g/cm3 + => Scor: 4.8708 + + ==> RESULTS OF REFINEMENT: + + + => No. of fitted parameters: 15 + + +------------------------------------------------------------------------------ + => Phase No. 1 Diamond F d -3 m:1 +------------------------------------------------------------------------------ + + => No. of reflections for pattern#: 1: 60 + + + ==> ATOM PARAMETERS: + + Name x sx y sy z sz B sB occ. socc. Mult + C 0.12500( 0) 0.12500( 0) 0.12500( 0) 0.893( 30) 1.000( 0) 16 + + ==> PROFILE PARAMETERS FOR PATTERN# 1 + + => Cell parameters : + 3.56700 0.00000 + 3.56700 0.00000 + 3.56700 0.00000 + 90.00000 0.00000 + 90.00000 0.00000 + 90.00000 0.00000 + + + => Overall scale factor : 0.101177976 0.000754629 + => T.O.F. Extinction parameter: 0.000000 0.000000 + => Overall temperature factor: 0.000000 0.000000 + => T.O.F. Gaussian variances Sig-2, Sig-1, Sig-0: + 0.000000 0.000000 + 4887.917969 530.093811 + 46937.718750 1715.570068 + + => T.O.F. Gaussian variance Sig-Q: 0.000000 0.000000 + => T.O.F. Isotropic Gaussian Strain parameter (G-strain): 0.00000 0.00000 + => T.O.F. Isotropic Gaussian Size parameter (G-size) : 0.00000 0.00000 + => T.O.F. Anisotropic Lorentzian Size parameter (Ani-LorSize): 0.00000 0.00000 + => T.O.F. Lorentzian FWHM Gam-2, Gam-1, Gam-0: + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + + => T.O.F. Lorentzian strain and size parameters (LStr,LSiz): + 0.000000 0.000000 + 0.000000 0.000000 + + => Direct cell parameters: + 3.567000 0.000000 + 3.567000 0.000000 + 3.567000 0.000000 + 90.000000 0.000000 + 90.000000 0.000000 + 90.000000 0.000000 + + => Preferred orientation parameters: + 0.000000 0.000000 + 0.000000 0.000000 + + => T.O.F. Peak shape parameter alpha0,beta0,beta1,alphaQ,betaQ: + 0.000000 0.000000 0.014330 + 0.001266 0.022544 0.002287 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + + + => Absorption parameters: + 0.00000 0.00000 + 0.00000 0.00000 + + + + ==> GLOBAL PARAMETERS FOR PATTERN# 1 + + + => Zero-point: 0.0000 0.0000 + => Background Parameters (linear interpolation) ==> + -0.228404 0.366523E-01 + 0.391510 0.314979E-01 + 0.695746 0.230111E-01 + 0.569209 0.178506E-01 + 0.302807 0.961624E-02 + 0.613633 0.109574E-01 + 0.737472 0.132017E-01 + 0.614094 0.389527E-01 + + => T.O.F.- dtt1 ( TOFo=dtt1*dsp ): 28385.86 4.50 + => T.O.F.- dtt2 (TOF=TOFo+dtt2*dsp*dsp ): 0.00 0.00 + => T.O.F.- dtt_1OverD (TOF=TOF+dtt_1overD/dsp): 0.00 0.00 + + ==> RELIABILITY FACTORS WITH ALL NON-EXCLUDED POINTS FOR PATTERN: 1 + + => Cycle:100 => MaxCycle:100 + => N-P+C: 1933 + => R-factors (not corrected for background) for Pattern: 1 + => Rp: 15.6 Rwp: 16.9 Rexp: 3.96 Chi2: 18.1 L.S. refinement + => Conventional Rietveld R-factors for Pattern: 1 + => Rp: 22.8 Rwp: 20.6 Rexp: 4.83 Chi2: 18.1 + => Deviance: 257. Dev* : 0.9772E-01 + => DW-Stat.: 0.3186 DW-exp: 1.8745 + => N-sigma of the GoF: 532.760 + + ==> RELIABILITY FACTORS FOR POINTS WITH BRAGG CONTRIBUTIONS FOR PATTERN: 1 + + => N-P+C: 1933 + => R-factors (not corrected for background) for Pattern: 1 + => Rp: 15.6 Rwp: 16.9 Rexp: 3.96 Chi2: 18.1 L.S. refinement + => Conventional Rietveld R-factors for Pattern: 1 + => Rp: 22.8 Rwp: 20.6 Rexp: 4.83 Chi2: 18.1 + => Deviance: 257. Dev* : 0.9772E-01 + => DW-Stat.: 0.3186 DW-exp: 1.8745 + => N-sigma of the GoF: 532.760 + + => Global user-weigthed Chi2 (Bragg contrib.): 18.1 + + ----------------------------------------------------- + BRAGG R-Factors and weight fractions for Pattern # 1 + ----------------------------------------------------- + + => Phase: 1 Diamond + => Bragg R-factor: 16.4 Vol: 45.385( 0.000) Fract(%): 100.00( 1.05) + => Rf-factor= 30.6 ATZ: 27673.344 Brindley: 1.0000 + + + CPU Time: 2.289 seconds + 0.038 minutes + + => Run finished at: Date: 24/06/2026 Time: 12:52:13.144 diff --git a/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.int b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.int new file mode 100644 index 000000000..30da5db33 --- /dev/null +++ b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.int @@ -0,0 +1,289 @@ +nuclear index +(3i4,2f12.4,i4,4f12.4) +0.0000 0 0 + -4 10 -3 0.1000 0.3700 1 1.1004 84.6734 0.0000 0.0000 + -4 11 -4 3.4800 1.1200 1 1.0977 94.4572 0.0000 0.0000 + -4 11 -3 28.3500 2.4400 1 1.0469 85.0464 0.0000 0.0000 + -4 12 -4 12.8000 1.5900 1 1.0440 94.0877 0.0000 0.0000 + -4 12 -3 19.8900 2.1400 1 0.9942 84.9083 0.0000 0.0000 + -3 8 -3 23.7400 1.1200 1 1.4877 94.7649 0.0000 0.0000 + -3 9 -3 0.1700 0.1500 1 1.3920 93.5571 0.0000 0.0000 + -3 10 -3 32.4900 1.5100 1 1.3004 92.9366 0.0000 0.0000 + -2 6 -2 0.5700 0.0900 1 2.0880 94.0963 0.0000 0.0000 + -1 3 -1 4.0900 0.0800 1 4.1760 93.8173 0.0000 0.0000 + -5 7 -4 1.1500 0.7800 1 1.0521 83.5762 0.0000 0.0000 + -5 8 -5 3.1100 1.1700 1 1.0616 92.9739 0.0000 0.0000 + -5 8 -4 0.4700 0.4900 1 1.0316 85.2773 0.0000 0.0000 + -5 9 -5 0.7300 0.5500 1 1.0356 93.2707 0.0000 0.0000 + -5 9 -4 0.3100 0.7600 1 1.0053 85.8520 0.0000 0.0000 + -5 10 -5 4.4900 1.3900 1 1.0057 94.6910 0.0000 0.0000 + -4 6 -4 1.9300 0.4700 1 1.3409 92.3963 0.0000 0.0000 + -4 7 -4 1.7600 0.4900 1 1.3032 93.8442 0.0000 0.0000 + -4 7 -3 3.3500 0.6900 1 1.2512 83.5796 0.0000 0.0000 + -4 8 -4 1.2900 0.5200 1 1.2571 94.6841 0.0000 0.0000 + -3 5 -3 2.2000 0.2900 1 1.7558 93.2672 0.0000 0.0000 + -3 6 -3 65.4800 1.2800 1 1.6761 94.6796 0.0000 0.0000 + -2 3 -2 8.3100 0.1800 1 2.6818 92.3998 0.0000 0.0000 + -2 4 -2 5.2100 0.1500 1 2.5141 94.6715 0.0000 0.0000 + -5 4 -6 0.2900 0.4000 1 1.1014 91.3409 0.0000 0.0000 + -5 4 -5 11.0800 1.5300 1 1.0950 84.4884 0.0000 0.0000 + -5 5 -6 4.6700 1.2100 1 1.1060 94.8469 0.0000 0.0000 + -5 5 -5 0.6000 0.4700 1 1.1006 87.3067 0.0000 0.0000 + -4 3 -4 7.0100 0.7200 1 1.3649 83.7538 0.0000 0.0000 + -4 4 -5 0.4000 0.2200 1 1.3802 96.1286 0.0000 0.0000 + -4 4 -4 4.0900 0.5900 1 1.3757 87.3216 0.0000 0.0000 + -3 3 -3 1.4000 0.1900 1 1.8343 87.5886 0.0000 0.0000 + -2 2 -2 36.8200 0.3400 1 2.7513 87.3102 0.0000 0.0000 + -4 12 -6 5.4500 1.2300 1 1.0794 110.3408 0.0000 0.0000 + -4 13 -6 4.6700 1.6400 1 1.0320 108.7783 0.0000 0.0000 + -3 9 -4 0.4000 0.2800 1 1.4346 105.2690 0.0000 0.0000 + -3 10 -5 4.4400 0.7500 1 1.3561 113.5557 0.0000 0.0000 + -3 11 -5 14.3800 1.2900 1 1.2791 111.7766 0.0000 0.0000 + -3 12 -5 7.4400 1.1100 1 1.2055 110.0480 0.0000 0.0000 + -2 6 -3 47.2500 0.6800 1 2.1589 110.3597 0.0000 0.0000 + -2 7 -3 119.5300 1.2000 1 1.9718 108.1326 0.0000 0.0000 + -5 9 -7 1.6800 0.8000 1 1.0402 107.8845 0.0000 0.0000 + -5 10 -7 3.6600 1.5800 1 1.0149 108.2621 0.0000 0.0000 + -4 8 -7 0.3500 0.5300 1 1.2317 117.2587 0.0000 0.0000 + -4 8 -6 2.6300 0.8700 1 1.2615 111.3933 0.0000 0.0000 + -4 9 -7 8.8300 1.3500 1 1.1961 118.2636 0.0000 0.0000 + -4 9 -6 0.2600 0.5000 1 1.2196 111.9691 0.0000 0.0000 + -4 10 -7 1.6500 0.7800 1 1.1569 117.6666 0.0000 0.0000 + -3 6 -5 0.6100 0.2400 1 1.6575 115.5765 0.0000 0.0000 + -3 6 -4 35.1100 1.0300 1 1.6955 106.2940 0.0000 0.0000 + -3 7 -5 9.4800 0.6800 1 1.5894 116.2612 0.0000 0.0000 + -3 7 -4 0.8800 0.2400 1 1.6130 106.7334 0.0000 0.0000 + -2 4 -3 21.5000 0.3200 1 2.5229 111.3864 0.0000 0.0000 + -5 5 -8 4.8100 1.3400 1 1.0664 106.4842 0.0000 0.0000 + -5 6 -9 7.7600 1.6600 1 1.0314 113.4084 0.0000 0.0000 + -5 6 -8 9.6100 1.9500 1 1.0641 108.6735 0.0000 0.0000 + -5 7 -9 2.7600 1.1700 1 1.0249 115.2791 0.0000 0.0000 + -5 7 -8 0.5300 0.6200 1 1.0556 110.9149 0.0000 0.0000 + -5 8 -9 2.7300 1.3100 1 1.0136 117.3790 0.0000 0.0000 + -4 4 -6 17.5200 1.5500 1 1.3508 103.8870 0.0000 0.0000 + -4 5 -7 0.4800 0.3400 1 1.2987 112.5375 0.0000 0.0000 + -4 5 -6 3.1400 0.6700 1 1.3450 106.9386 0.0000 0.0000 + -4 6 -7 0.9400 0.6400 1 1.2847 115.5404 0.0000 0.0000 + -3 4 -5 1.0000 0.1800 1 1.7488 111.6351 0.0000 0.0000 + -2 2 -3 3.5300 0.1500 1 2.7018 103.9133 0.0000 0.0000 + -3 13 -8 0.7400 0.6400 1 1.1069 130.2385 0.0000 0.0000 + -3 14 -9 0.4900 0.8300 1 1.0342 133.8154 0.0000 0.0000 + -3 14 -8 9.1100 2.0600 1 1.0586 128.4634 0.0000 0.0000 + -2 8 -5 0.6600 0.2100 1 1.7582 128.9825 0.0000 0.0000 + -2 9 -6 0.3600 0.1900 1 1.5827 135.7394 0.0000 0.0000 + -2 9 -5 12.1600 0.7500 1 1.6401 126.0656 0.0000 0.0000 + -2 10 -6 0.4700 0.2900 1 1.4891 131.7035 0.0000 0.0000 + -2 11 -7 0.4300 0.3900 1 1.3570 136.7857 0.0000 0.0000 + -2 11 -6 13.4500 1.1300 1 1.3992 129.0175 0.0000 0.0000 + -2 12 -7 3.3900 0.7700 1 1.2841 133.2860 0.0000 0.0000 + -1 5 -3 42.1600 0.3900 1 2.9785 132.1115 0.0000 0.0000 + -4 10 -10 3.4200 1.4100 1 1.0502 134.1552 0.0000 0.0000 + -4 10 -9 2.0500 1.0900 1 1.0910 129.2341 0.0000 0.0000 + -4 11 -9 5.3500 1.4500 1 1.0607 129.0702 0.0000 0.0000 + -4 12 -9 1.2700 0.8700 1 1.0286 128.6565 0.0000 0.0000 + -3 8 -8 4.0400 0.8000 1 1.3428 136.1571 0.0000 0.0000 + -3 8 -7 1.4700 0.6000 1 1.4119 130.4636 0.0000 0.0000 + -3 9 -8 2.9800 0.7700 1 1.3000 136.2064 0.0000 0.0000 + -3 10 -9 3.7800 0.9700 1 1.1997 140.2005 0.0000 0.0000 + -3 10 -8 0.7200 0.6000 1 1.2536 134.6193 0.0000 0.0000 + -3 11 -9 3.8000 1.2800 1 1.1598 139.4247 0.0000 0.0000 + -2 5 -5 6.9200 0.3400 1 2.1002 133.1812 0.0000 0.0000 + -2 6 -6 0.1700 0.0900 1 1.8558 141.1355 0.0000 0.0000 + -2 6 -5 11.9300 0.4800 1 1.9950 133.3468 0.0000 0.0000 + -2 7 -6 0.2900 0.1600 1 1.7700 139.2534 0.0000 0.0000 + -1 3 -3 0.8400 0.0500 1 3.7116 140.5265 0.0000 0.0000 + -4 6 -10 0.4900 0.7000 1 1.1158 127.5221 0.0000 0.0000 + -4 6 -9 1.4900 0.7100 1 1.1746 124.0425 0.0000 0.0000 + -4 7 -11 1.4900 0.8700 1 1.0518 132.2902 0.0000 0.0000 + -4 7 -10 5.4800 1.4900 1 1.1064 130.0769 0.0000 0.0000 + -4 7 -9 7.9500 1.4900 1 1.1614 126.5446 0.0000 0.0000 + -4 8 -11 3.6400 1.5800 1 1.0406 134.7883 0.0000 0.0000 + -4 8 -10 1.2800 1.1500 1 1.0918 131.9986 0.0000 0.0000 + -3 5 -9 0.6500 0.3500 1 1.3347 134.1879 0.0000 0.0000 + -3 5 -8 17.8100 1.2100 1 1.4306 131.1397 0.0000 0.0000 + -3 5 -7 0.7100 0.2900 1 1.5303 127.0597 0.0000 0.0000 + -3 6 -9 19.4900 1.6000 1 1.3211 137.1776 0.0000 0.0000 + -3 6 -8 5.4400 0.8000 1 1.4102 133.6842 0.0000 0.0000 + -2 3 -5 3.1500 0.2000 1 2.2319 127.7123 0.0000 0.0000 + -2 4 -6 84.7700 1.2300 1 1.9817 137.2681 0.0000 0.0000 + -2 4 -5 82.6200 0.9800 1 2.1834 131.8531 0.0000 0.0000 + -1 2 -3 38.0800 0.3200 1 3.9632 137.1919 0.0000 0.0000 + 1 5 -5 59.7500 0.5800 1 2.4439 144.0943 0.0000 0.0000 + 1 6 -6 2.5100 0.2000 1 2.0744 148.3055 0.0000 0.0000 + 1 7 -7 5.9200 0.4300 1 1.7980 151.1125 0.0000 0.0000 + 1 8 -8 6.7500 0.6700 1 1.5848 153.8105 0.0000 0.0000 + 1 8 -7 1.1200 0.2300 1 1.7059 148.4912 0.0000 0.0000 + 1 9 -9 11.6300 1.0900 1 1.4157 155.5265 0.0000 0.0000 + 1 9 -8 4.9700 0.5800 1 1.5131 150.7120 0.0000 0.0000 + 2 10 -11 6.9800 1.3700 1 1.1560 147.1447 0.0000 0.0000 + 2 10 -10 2.0100 0.6000 1 1.2219 143.7356 0.0000 0.0000 + 2 11 -12 0.8300 0.7900 1 1.0660 148.5628 0.0000 0.0000 + 2 11 -11 2.1700 0.8700 1 1.1225 146.0796 0.0000 0.0000 + 2 11 -10 0.3400 0.5400 1 1.1803 142.9071 0.0000 0.0000 + 2 12 -12 2.4700 1.4500 1 1.0371 148.4304 0.0000 0.0000 + 1 5 -9 3.2200 0.4800 1 1.5887 151.7089 0.0000 0.0000 + 1 5 -8 2.8500 0.3400 1 1.7572 152.2418 0.0000 0.0000 + 1 5 -7 3.1000 0.2500 1 1.9554 151.5897 0.0000 0.0000 + 1 6 -10 0.4700 0.3700 1 1.4264 155.0939 0.0000 0.0000 + 1 6 -9 3.6700 0.5400 1 1.5587 155.1381 0.0000 0.0000 + 1 6 -8 4.7700 0.4500 1 1.7106 154.7691 0.0000 0.0000 + 1 7 -11 7.2900 1.2800 1 1.2924 157.3187 0.0000 0.0000 + 1 7 -10 1.3300 0.5400 1 1.3985 157.8711 0.0000 0.0000 + 1 7 -9 15.1000 1.0300 1 1.5181 157.0197 0.0000 0.0000 + 1 8 -13 0.9300 0.7700 1 1.1024 158.9683 0.0000 0.0000 + 1 8 -12 5.7400 1.3200 1 1.1802 159.3636 0.0000 0.0000 + 1 8 -11 1.1500 0.6400 1 1.2670 160.0116 0.0000 0.0000 + 1 9 -14 2.7800 1.1900 1 1.0198 160.2546 0.0000 0.0000 + 1 9 -13 1.1600 0.8300 1 1.0853 161.1329 0.0000 0.0000 + 1 9 -12 3.7500 1.1500 1 1.1574 160.8069 0.0000 0.0000 + 1 10 -14 2.5300 1.5100 1 1.0040 162.2095 0.0000 0.0000 + 1 10 -13 1.5000 1.0100 1 1.0649 162.0399 0.0000 0.0000 + 0 2 -6 13.2500 0.2800 1 2.4660 147.9515 0.0000 0.0000 + 0 3 -9 7.4400 0.6000 1 1.6441 148.1451 0.0000 0.0000 + 0 3 -8 9.0900 0.4800 1 1.8508 150.7784 0.0000 0.0000 + 0 4 -12 1.0500 0.6000 1 1.2330 147.6237 0.0000 0.0000 + 0 4 -11 1.1100 0.5700 1 1.3462 150.6547 0.0000 0.0000 + 0 5 -14 0.6800 0.6900 1 1.0574 149.6646 0.0000 0.0000 + 0 5 -13 5.1300 1.3700 1 1.1389 151.8619 0.0000 0.0000 + 1 5 -13 0.4300 0.8900 1 1.1273 147.0989 0.0000 0.0000 + 1 5 -12 1.1000 0.8000 1 1.2180 147.9984 0.0000 0.0000 + 1 6 -14 1.7600 1.1100 1 1.0472 149.9711 0.0000 0.0000 + 1 3 -3 8.3100 0.1300 1 3.6743 126.9720 0.0000 0.0000 + 2 5 -6 14.1400 0.4800 1 1.9146 125.9212 0.0000 0.0000 + 2 6 -7 11.4100 0.6300 1 1.7077 132.7813 0.0000 0.0000 + 2 6 -6 55.7600 1.0200 1 1.8371 126.6506 0.0000 0.0000 + 2 7 -8 0.7900 0.3400 1 1.5325 137.1409 0.0000 0.0000 + 2 7 -7 0.3500 0.1700 1 1.6420 133.4453 0.0000 0.0000 + 3 8 -10 33.3600 2.4000 1 1.1955 130.2694 0.0000 0.0000 + 3 8 -9 1.0000 0.5100 1 1.2605 126.7577 0.0000 0.0000 + 3 9 -11 2.2600 1.1600 1 1.1096 134.7883 0.0000 0.0000 + 3 9 -10 1.0000 0.7700 1 1.1676 130.6023 0.0000 0.0000 + 3 9 -9 3.4100 0.7700 1 1.2248 126.7188 0.0000 0.0000 + 3 10 -12 0.7000 1.0200 1 1.0327 136.7226 0.0000 0.0000 + 3 10 -11 2.0000 0.7700 1 1.0842 134.4778 0.0000 0.0000 + 3 10 -10 5.0700 1.0500 1 1.1356 131.2492 0.0000 0.0000 + 3 11 -11 0.9600 0.6500 1 1.0558 134.0395 0.0000 0.0000 + 1 2 -4 22.3300 0.2400 1 3.2709 130.7450 0.0000 0.0000 + 1 3 -5 30.3100 0.3800 1 2.7001 140.7396 0.0000 0.0000 + 2 4 -9 3.0000 0.5000 1 1.4937 132.8214 0.0000 0.0000 + 2 4 -8 16.4900 0.8000 1 1.6355 130.7730 0.0000 0.0000 + 2 4 -7 0.5900 0.1700 1 1.7957 128.0807 0.0000 0.0000 + 2 5 -10 11.4500 1.1200 1 1.3649 137.7878 0.0000 0.0000 + 2 5 -9 2.3200 0.4800 1 1.4827 136.4992 0.0000 0.0000 + 2 5 -8 1.7100 0.3100 1 1.6150 134.2033 0.0000 0.0000 + 2 6 -11 1.1500 0.6900 1 1.2519 141.8477 0.0000 0.0000 + 2 6 -10 19.5900 1.5500 1 1.3500 141.0043 0.0000 0.0000 + 2 6 -9 1.2100 0.5200 1 1.4594 139.2007 0.0000 0.0000 + 3 5 -12 11.8500 1.7800 1 1.0927 127.7266 0.0000 0.0000 + 3 6 -13 2.1500 1.1300 1 1.0259 131.5225 0.0000 0.0000 + 3 6 -12 7.8400 1.5500 1 1.0903 130.7587 0.0000 0.0000 + 3 6 -11 4.1100 1.0600 1 1.1602 129.3000 0.0000 0.0000 + 3 7 -12 0.3800 0.6300 1 1.0824 133.8040 0.0000 0.0000 + 1 1 -6 16.2300 0.3500 1 2.2847 124.7919 0.0000 0.0000 + 1 2 -9 5.8100 0.5400 1 1.5892 133.4923 0.0000 0.0000 + 1 2 -8 18.7800 0.7500 1 1.7825 133.9260 0.0000 0.0000 + 1 2 -7 3.1400 0.2500 1 2.0247 134.4296 0.0000 0.0000 + 1 2 -6 0.0600 0.0300 1 2.3348 133.6791 0.0000 0.0000 + 2 2 -13 10.0100 1.7200 1 1.0607 125.0859 0.0000 0.0000 + 2 2 -12 2.0900 0.9100 1 1.1424 124.6808 0.0000 0.0000 + 2 3 -14 1.2600 0.9800 1 1.0033 130.1537 0.0000 0.0000 + 2 3 -13 1.3700 0.8300 1 1.0758 130.6172 0.0000 0.0000 + 2 3 -12 6.0900 1.1600 1 1.1586 129.8603 0.0000 0.0000 + 2 3 -11 1.5600 0.6300 1 1.2536 129.4254 0.0000 0.0000 + 2 4 -13 1.5400 1.0900 1 1.0849 134.4251 0.0000 0.0000 + 2 4 -12 1.2000 0.9400 1 1.1674 133.7432 0.0000 0.0000 + 2 5 -14 0.7500 0.8800 1 1.0168 138.1447 0.0000 0.0000 + 2 3 -4 27.2200 0.3700 1 2.3831 104.7092 0.0000 0.0000 + 2 4 -5 3.7300 0.2100 1 2.1497 117.2272 0.0000 0.0000 + 3 5 -7 0.2600 0.1600 1 1.5006 112.5450 0.0000 0.0000 + 3 5 -6 86.7100 1.6400 1 1.5744 105.9433 0.0000 0.0000 + 3 6 -7 5.5000 0.6100 1 1.4702 114.3549 0.0000 0.0000 + 4 6 -8 0.2400 0.3600 1 1.1917 105.0312 0.0000 0.0000 + 4 7 -9 23.2800 2.0500 1 1.1353 111.6603 0.0000 0.0000 + 4 7 -8 0.0400 0.3200 1 1.1742 106.2699 0.0000 0.0000 + 4 8 -9 5.5900 1.1600 1 1.1157 112.9770 0.0000 0.0000 + 1 1 -3 14.4400 0.1700 1 3.9718 113.8691 0.0000 0.0000 + 2 2 -6 17.3800 0.4800 1 1.9859 113.8926 0.0000 0.0000 + 2 2 -5 8.1500 0.2500 1 2.1982 107.9796 0.0000 0.0000 + 2 3 -6 0.7500 0.1400 1 1.9976 119.6433 0.0000 0.0000 + 3 2 -8 3.9000 0.6100 1 1.3950 105.6059 0.0000 0.0000 + 3 3 -9 2.0200 0.6000 1 1.3239 113.5969 0.0000 0.0000 + 3 3 -8 22.0900 1.2500 1 1.4178 110.2715 0.0000 0.0000 + 3 3 -7 3.2300 0.4400 1 1.5125 105.4214 0.0000 0.0000 + 3 4 -9 3.1200 0.7200 1 1.3322 117.7050 0.0000 0.0000 + 3 4 -8 0.3800 0.2600 1 1.4242 113.9080 0.0000 0.0000 + 4 3 -11 1.2900 0.7200 1 1.0340 107.2869 0.0000 0.0000 + 4 4 -12 1.2700 0.8600 1 0.9930 113.6273 0.0000 0.0000 + 4 4 -11 13.3900 1.8600 1 1.0455 111.4008 0.0000 0.0000 + 4 4 -10 0.3200 0.4800 1 1.0991 107.9859 0.0000 0.0000 + 4 5 -12 0.9500 0.8300 1 0.9985 117.1429 0.0000 0.0000 + 4 5 -11 1.1600 0.9500 1 1.0505 113.7000 0.0000 0.0000 + 4 5 -10 3.1300 1.1200 1 1.1032 111.0450 0.0000 0.0000 + 4 6 -11 6.4800 1.5000 1 1.0492 116.9590 0.0000 0.0000 + 1 0 -4 1.0600 0.0600 1 3.0298 106.5404 0.0000 0.0000 + 2 0 -8 0.2000 0.1600 1 1.5150 106.0751 0.0000 0.0000 + 2 1 -9 1.2800 0.3500 1 1.4359 115.7696 0.0000 0.0000 + 2 1 -8 0.4600 0.1800 1 1.5778 113.9435 0.0000 0.0000 + 2 1 -7 17.6000 0.7200 1 1.7428 111.0215 0.0000 0.0000 + 3 0 -12 16.0500 2.2400 1 1.0099 106.5300 0.0000 0.0000 + 3 0 -11 0.7500 0.4800 1 1.0750 104.7550 0.0000 0.0000 + 3 1 -12 0.4100 0.6600 1 1.0394 110.6593 0.0000 0.0000 + 3 2 -12 5.1300 1.2600 1 1.0626 116.1351 0.0000 0.0000 + 3 2 -11 11.3000 1.6100 1 1.1355 114.3807 0.0000 0.0000 + 2 2 -3 8.3700 0.1700 1 2.5017 86.2479 0.0000 0.0000 + 3 4 -5 40.3400 0.9800 1 1.6531 94.8577 0.0000 0.0000 + 3 4 -4 7.4300 0.3500 1 1.6529 84.4992 0.0000 0.0000 + 4 4 -6 33.4700 1.6800 1 1.2508 86.2502 0.0000 0.0000 + 4 5 -7 0.8300 0.4500 1 1.2351 96.0380 0.0000 0.0000 + 4 5 -6 104.9200 2.6600 1 1.2500 89.0176 0.0000 0.0000 + 5 5 -8 2.3300 0.9500 1 0.9982 89.2531 0.0000 0.0000 + 5 6 -8 6.5600 1.3000 1 0.9987 91.6950 0.0000 0.0000 + 5 6 -7 11.5000 1.4900 1 0.9994 85.0928 0.0000 0.0000 + 3 1 -6 0.1500 0.2000 1 1.5163 88.7013 0.0000 0.0000 + 3 2 -6 24.0400 0.9100 1 1.5719 94.6916 0.0000 0.0000 + 4 1 -8 9.5500 1.2400 1 1.1234 87.0054 0.0000 0.0000 + 4 2 -9 4.3700 0.9600 1 1.1167 96.6631 0.0000 0.0000 + 4 2 -8 0.2400 0.3500 1 1.1608 92.1265 0.0000 0.0000 + 4 2 -7 24.9000 1.5400 1 1.1928 85.8423 0.0000 0.0000 + 4 3 -8 34.6500 2.0400 1 1.1859 95.8169 0.0000 0.0000 + 2 -1 -6 0.1800 0.1000 1 1.6929 89.3791 0.0000 0.0000 + 2 0 -5 0.0500 0.0400 1 2.0046 92.0967 0.0000 0.0000 + 3 -1 -10 0.1600 0.3400 1 1.0964 95.7441 0.0000 0.0000 + 3 -1 -9 23.4900 1.7200 1 1.1619 92.2382 0.0000 0.0000 + 3 -1 -8 0.9200 0.4400 1 1.2268 88.2888 0.0000 0.0000 + 3 0 -8 1.5200 0.5100 1 1.2984 94.5289 0.0000 0.0000 + 4 0 -10 2.0600 0.8000 1 1.0023 91.5386 0.0000 0.0000 + 2 2 -2 3.5400 0.1000 1 2.3314 67.1295 0.0000 0.0000 + 3 2 -3 91.2200 1.3200 1 1.5014 61.9052 0.0000 0.0000 + 3 3 -3 9.5800 0.4500 1 1.5542 67.1719 0.0000 0.0000 + 4 3 -5 1.1500 0.3400 1 1.2144 73.7689 0.0000 0.0000 + 4 3 -4 0.5900 0.3900 1 1.1399 62.6489 0.0000 0.0000 + 4 4 -4 42.1200 1.6400 1 1.1656 67.1701 0.0000 0.0000 + 2 0 -3 0.0500 0.0200 1 2.1656 68.3080 0.0000 0.0000 + 3 0 -4 8.5000 0.5100 1 1.4070 62.5813 0.0000 0.0000 + 3 1 -4 3.1000 0.3000 1 1.5375 69.5296 0.0000 0.0000 + 4 0 -6 54.0600 2.2700 1 1.0828 68.3149 0.0000 0.0000 + 4 1 -6 1.4400 0.4700 1 1.1512 73.4205 0.0000 0.0000 + 4 1 -5 8.7800 0.8800 1 1.1137 64.9528 0.0000 0.0000 + 2 -1 -4 1.2500 0.1200 1 1.8920 71.6530 0.0000 0.0000 + 3 -2 -7 6.7700 0.8000 1 1.1816 75.3990 0.0000 0.0000 + 3 -2 -6 26.0500 1.2900 1 1.1956 68.0680 0.0000 0.0000 + 3 2 -2 1.7400 0.2800 1 1.2081 45.1577 0.0000 0.0000 + 3 3 -2 331.0700 2.6800 1 1.2942 50.7262 0.0000 0.0000 + 4 4 -3 0.9300 0.3900 1 1.0320 55.0177 0.0000 0.0000 + 1 0 -1 0.0400 0.0100 1 3.6860 48.1858 0.0000 0.0000 + 2 0 -2 155.3200 0.7700 1 1.8430 48.1686 0.0000 0.0000 + 3 -1 -3 15.8100 0.9000 1 1.0249 40.0767 0.0000 0.0000 + 3 0 -3 0.3200 0.1400 1 1.2287 47.6013 0.0000 0.0000 + 2 -3 -4 51.3800 1.1700 1 1.2670 49.9018 0.0000 0.0000 + 1 -1 -1 42.4900 0.2400 1 1.7445 23.8476 0.0000 0.0000 + 1 -4 -3 29.9200 0.8600 1 1.0294 32.0942 0.0000 0.0000 + 1 8 -2 113.9600 1.0300 1 1.8687 89.2926 0.0000 0.0000 + 1 9 -2 14.5800 0.5600 1 1.6479 86.4255 0.0000 0.0000 + 1 10 -2 6.0300 0.5100 1 1.4684 84.1446 0.0000 0.0000 + 1 11 -3 6.0100 0.5900 1 1.4342 95.2840 0.0000 0.0000 + 1 12 -3 0.3300 0.2000 1 1.3031 92.7149 0.0000 0.0000 + 1 13 -3 9.2700 1.0700 1 1.1912 90.1452 0.0000 0.0000 + 1 14 -3 0.6200 0.3900 1 1.0951 88.4383 0.0000 0.0000 + 1 15 -4 1.0400 0.6300 1 1.0694 96.9565 0.0000 0.0000 + 1 15 -3 2.3700 0.8600 1 1.0117 86.7223 0.0000 0.0000 diff --git a/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.out b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.out new file mode 100644 index 000000000..99d22c55c --- /dev/null +++ b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.out @@ -0,0 +1,707 @@ + + + ********************************************************** + ** 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: 24/06/2026 Time: 10:01:33.360 + + => PCR file code: taurine + => DAT file code: taurine -> Relative contribution: 1.0000 + + ==> CONDITIONS OF THIS RUN FOR PATTERN No.: 1 + + => Refinement/Calculation of Neutron integrated intensity(Laue or monochromatic) data or Flipping Ratios + => Neutron Time-Of-Flight data + + ==> INPUT/OUTPUT OPTIONS: + + => Generate new input file *.PCR + + => Number of cycles: 20 + => Relaxation factors ==> for coordinates: 1.00 + => for anisotropic temperature factors: 1.00 + => EPS-value for convergence: 0.1 + => Number of Least-Squares parameters varied: 0 + -------------------------------------------------------------------------------- + => Phase No. 1 + taurine + -------------------------------------------------------------------------------- + =>-------> Pattern# 1 + => Integrated intensities or Flipping Ratios as observations for phase: 1 + => Crystal Structure Refinement + + =>-------> Data for PHASE: 1 + => Number of atoms: 14 + => Number of distance constraints: 0 + => Number of angle constraints: 0 + + => Symmetry information on space group: P 21/c + -> The multiplicity of the general position is: 4 + -> The space group is Centric (-1 at origin) + -> Lattice type P: { 000 } + -> Reduced set of symmetry operators: + + No. IT Symmetry symbol Rotation part Associated Translation + 1: ( 1) 1 --> ( x, y, z) + { 0.0000 0.0000 0.0000} + 2: ( 3) 2 ( 0, y, 0) --> (-x, y,-z) + { 0.0000 0.5000 0.5000} + + + Information on Space Group: + --------------------------- + + => Number of Space group: 14 + => Hermann-Mauguin Symbol: P 21/c + => Hall Symbol: -P 2ybc + => Table Setting Choice: b1 + => Setting Type: IT (Generated from Hermann-Mauguin symbol) + => Crystal System: Monoclinic + => Laue Class: 2/m + => Point Group: 2/m + => Bravais Lattice: P + => Lattice Symbol: mP + => Reduced Number of S.O.: 2 + => General multiplicity: 4 + => Centrosymmetry: Centric (-1 at origin) + => Generators (exc. -1&L): 1 + => Asymmetric unit: 0.000 <= x <= 1.000 + 0.000 <= y <= 0.250 + 0.000 <= z <= 1.000 + => Centring vectors: 0 + + + => List of all Symmetry Operators and Symmetry Symbols + + => SYMM( 1): x,y,z Symbol: 1 + => SYMM( 2): -x,y+1/2,-z+1/2 Symbol: 2 (0,1/2,0) 0,y,1/4 + => SYMM( 3): -x,-y,-z Symbol: -1 0,0,0 + => SYMM( 4): x,-y+1/2,z+1/2 Symbol: c x,1/4,z + + => Special Wyckoff Positions for P 21/c + + Multp Site Representative Coordinates (centring translations excluded) + 2 d 1/2,0,1/2 1/2,1/2,0 + + 2 c 0,0,1/2 0,1/2,0 + + 2 b 1/2,0,0 1/2,1/2,1/2 + + 2 a 0,0,0 0,1/2,1/2 + + + => Initial parameters ==> + Atom Ntyp X Y Z B occ. in fin Spc Mult + B11 B22 B33 B12 B13 B23 + S1 S 0.19448 0.35173 0.34730 1.37018 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + O1 O 0.31207 0.23951 0.35143 2.68011 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + O2 O -0.05909 0.33563 0.29636 3.50515 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + O3 O 0.22105 0.41215 0.50573 1.83513 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + N1 N 0.26340 0.62808 0.33048 2.07364 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + H1 H 0.12861 0.58669 0.41769 3.31527 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + H2 H 0.18953 0.71385 0.31124 4.46988 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + H3 H 0.43970 0.62023 0.34592 4.34151 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + C1 C 0.34384 0.44116 0.20155 1.73667 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + H11 H 0.55246 0.43345 0.24304 3.32279 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + H12 H 0.32537 0.38970 0.08264 3.05746 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + C2 C 0.20029 0.55716 0.18272 1.66017 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + H21 H 0.27650 0.60004 0.07688 2.15403 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + H22 H -0.00383 0.54767 0.15762 4.71303 1.00000 0 0 0 4 + Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 + + => It is assumed that THE FIRST GIVEN SITE plus all the other atoms + occupying THE SAME POSITION have a total full occupation (no vacancies!) + (if this is not the case, change the order of atoms to obtain correct values for the content of the unit cell) + The given occupation factors have been obtained mutiplying m/M by 1.0000 + -> Atom: S , Chemical element: S Atomic Mass: 32.0600 + -> Atom: O , Chemical element: O Atomic Mass: 15.9994 + -> Atom: O , Chemical element: O Atomic Mass: 15.9994 + -> Atom: O , Chemical element: O Atomic Mass: 15.9994 + -> Atom: N , Chemical element: N Atomic Mass: 14.0067 + -> Atom: H , Chemical element: H Atomic Mass: 1.0080 + -> Atom: H , Chemical element: H Atomic Mass: 1.0080 + -> Atom: H , Chemical element: H Atomic Mass: 1.0080 + -> Atom: C , Chemical element: C Atomic Mass: 12.0110 + -> Atom: H , Chemical element: H Atomic Mass: 1.0080 + -> Atom: H , Chemical element: H Atomic Mass: 1.0080 + -> Atom: C , Chemical element: C Atomic Mass: 12.0110 + -> Atom: H , Chemical element: H Atomic Mass: 1.0080 + -> Atom: H , Chemical element: H Atomic Mass: 1.0080 + => The given value of ATZ is 500.57 the program has calculated: 500.57 + The value of ATZ given in the input PCR file will be used for quantitative analysis + => The chemical content of the unit cell is: + 4.0000 S + 4.0000 O + 4.0000 O + 4.0000 O + 4.0000 N + 4.0000 H + 4.0000 H + 4.0000 H + 4.0000 C + 4.0000 H + + 4.0000 H + 4.0000 C + 4.0000 H + 4.0000 H + => The normalized site occupation numbers in % are: + 100.0000 S1 : 100.0000 O1 : 100.0000 O2 : 100.0000 O3 : 100.0000 N1 : 100.0000 H1 : 100.0000 H2 : 100.0000 H3 : 100.0000 C1 : 100.0000 H11 : + 100.0000 H12 : 100.0000 C2 : 100.0000 H21 : 100.0000 H22 + => The density (volumic mass) of the compound is: 1.730 g/cm3 + + =>-------> SCALE FACTORS, EXTINCTION AND CELL PARAMETERS FOR PATTERN: 1 + + => Scale factors ( 1: 6) : 2.71100 0.00000 0.00000 0.00000 0.00000 0.00000 + + => Extinction parameters: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + => Direct cell parameters: 5.2729 11.6565 7.8383 90.0000 94.0110 90.0000 + => Lambda/2 parameters: 0.0000 + + + ==> CODEWORDS FOR Scale and Extinction PARAMETERS for Pattern 1 + + => Scale factors ( 1: 6): 0.000 0.000 0.000 0.000 0.000 0.000 + + => Extinction parameters: 0.000 0.000 0.000 0.000 0.000 0.000 0.000 + + + => Cell constraints according to Laue symmetry: 2/m + + Metric information: + ------------------- + + => Direct cell parameters: + + a = 5.2729 b = 11.6565 c = 7.8383 + alpha = 90.000 beta = 94.011 gamma = 90.000 + Direct Cell Volume = 480.5893 + + => Reciprocal cell parameters: + + a*= 0.190115 b*= 0.085789 c*= 0.127892 + alpha*= 90.000 beta*= 85.989 gamma*= 90.000 + Reciprocal Cell Volume = 0.00208078 + + => Direct and Reciprocal Metric Tensors: + + GD GR + 27.8035 0.0000 -2.8910 0.036144 0.000000 0.001701 + 0.0000 135.8738 0.0000 0.000000 0.007360 0.000000 + -2.8910 0.0000 61.4389 0.001701 0.000000 0.016356 + + => Cartesian frame: x // a; z is along c*; y is within the ab-plane + + Crystal_to_Orthonormal_Matrix Orthonormal_to_Crystal Matrix + Cr_Orth_cel Orth_Cr_cel + 5.2729 0.0000 -0.5483 0.189649 -0.000000 0.013298 + 0.0000 11.6565 0.0000 0.000000 0.085789 -0.000000 + 0.0000 0.0000 7.8191 0.000000 0.000000 0.127892 + + Busing-Levy B-matrix: Hc=B.H Inverse of the Busing-Levy B-matrix + BL_M BL_Minv + 0.190115 0.000000 0.008946 5.2600 -0.0000 -0.3688 + 0.000000 0.085789 -0.000000 0.0000 11.6565 0.0000 + 0.000000 0.000000 0.127579 0.0000 0.0000 7.8383 + => Header of the Integrated Intensity file: + -> Title: nuclear index + -> Format of data: (3i4,2f12.4,i4,4f12.4) + -> T.O.F. Single Xtal data + -> Extinction correction of type: Shelx-like Isotropic + -> Type of data: F2 and Sig(F2) have been input + -> Reflection: ( 3 0 -11) of domain 1 is forbidden (excluded) + -> Reflection: ( 2 0 -5) of domain 1 is forbidden (excluded) + -> Reflection: ( 2 0 -3) of domain 1 is forbidden (excluded) + -> Reflection: ( 1 0 -1) of domain 1 is forbidden (excluded) + -> Reflection: ( 3 0 -3) of domain 1 is forbidden (excluded) + -> Reflections included only when F2> 3.0* sF2 + -> Nobserv (I>n*sigma): 171 -> Total Number of reflections: 286 + -> SumF: 603.1 SumF2: 3166.3 SumF2w: 267030.8 + + => Weighting Scheme: + => Conventional weight: w(H)=1.0/Variance(GobsH) + + => Scattering coefficients from internal table + + => Scattering lengths: + + S 0.2847 + O 0.5803 + N 0.9360 + H -0.3739 + C 0.6646 + + + => No optimization for routine tasks + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + => CYCLE No.: 1 + ------------------------------------------------------------------------------------------------------------------------------------ + => Phase 1 Name: taurine + ------------------------------------------------------------------------------------------------------------------------------------ + => New parameters, shifts, and standard deviations + + Atom x dx sx y dy sy z dz sz B dB sB occ. docc. socc. + + S1 0.19448 0.00000 0.00000 0.35173 0.00000 0.00000 0.34730 0.00000 0.00000 1.37018 0.00000 0.00000 1.00000 0.00000 0.00000 + O1 0.31207 0.00000 0.00000 0.23951 0.00000 0.00000 0.35143 0.00000 0.00000 2.68011 0.00000 0.00000 1.00000 0.00000 0.00000 + O2 -0.05909 0.00000 0.00000 0.33563 0.00000 0.00000 0.29636 0.00000 0.00000 3.50515 0.00000 0.00000 1.00000 0.00000 0.00000 + O3 0.22105 0.00000 0.00000 0.41215 0.00000 0.00000 0.50573 0.00000 0.00000 1.83513 0.00000 0.00000 1.00000 0.00000 0.00000 + N1 0.26340 0.00000 0.00000 0.62808 0.00000 0.00000 0.33048 0.00000 0.00000 2.07364 0.00000 0.00000 1.00000 0.00000 0.00000 + H1 0.12861 0.00000 0.00000 0.58669 0.00000 0.00000 0.41769 0.00000 0.00000 3.31527 0.00000 0.00000 1.00000 0.00000 0.00000 + H2 0.18953 0.00000 0.00000 0.71385 0.00000 0.00000 0.31124 0.00000 0.00000 4.46988 0.00000 0.00000 1.00000 0.00000 0.00000 + H3 0.43970 0.00000 0.00000 0.62023 0.00000 0.00000 0.34592 0.00000 0.00000 4.34151 0.00000 0.00000 1.00000 0.00000 0.00000 + C1 0.34384 0.00000 0.00000 0.44116 0.00000 0.00000 0.20155 0.00000 0.00000 1.73667 0.00000 0.00000 1.00000 0.00000 0.00000 + H11 0.55246 0.00000 0.00000 0.43345 0.00000 0.00000 0.24304 0.00000 0.00000 3.32279 0.00000 0.00000 1.00000 0.00000 0.00000 + H12 0.32537 0.00000 0.00000 0.38970 0.00000 0.00000 0.08264 0.00000 0.00000 3.05746 0.00000 0.00000 1.00000 0.00000 0.00000 + C2 0.20029 0.00000 0.00000 0.55716 0.00000 0.00000 0.18272 0.00000 0.00000 1.66017 0.00000 0.00000 1.00000 0.00000 0.00000 + H21 0.27650 0.00000 0.00000 0.60004 0.00000 0.00000 0.07688 0.00000 0.00000 2.15403 0.00000 0.00000 1.00000 0.00000 0.00000 + H22 -0.00383 0.00000 0.00000 0.54767 0.00000 0.00000 0.15762 0.00000 0.00000 4.71303 0.00000 0.00000 1.00000 0.00000 0.00000 + + ==> SCALE, EXTINCTION, CELL PARAMETERS FOR PATTERN# 1 + + => Scale factors ( 1: 6): + 2.711000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + + + => Extinction Parameters: + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + + + => Lambda/2 param: + 0.000000 0.000000 0.000000 + + => Global user-weigthed Chi2 (Bragg contrib.): 24.4 + + => ---------> Pattern# 1 + => Phase: 1 + => RF2 -factor : 18.3 + => RF2w-factor : 12.5 + => RF -factor : 14.4 + => Chi2(Intens): 24.4 + => N_eff Reflect.: 171 with I > 3.00 sigma + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + + => CYCLE No.: 1 + => Convergence reached at this CYCLE !!!! + => Parameter shifts set to zero + ------------------------------------------------------------------------------------------------------------------------------------ + => Phase 1 Name: taurine + ------------------------------------------------------------------------------------------------------------------------------------ + => New parameters, shifts, and standard deviations + + Atom x dx sx y dy sy z dz sz B dB sB occ. docc. socc. + + S1 0.19448 0.00000 0.00000 0.35173 0.00000 0.00000 0.34730 0.00000 0.00000 1.37018 0.00000 0.00000 1.00000 0.00000 0.00000 + O1 0.31207 0.00000 0.00000 0.23951 0.00000 0.00000 0.35143 0.00000 0.00000 2.68011 0.00000 0.00000 1.00000 0.00000 0.00000 + O2 -0.05909 0.00000 0.00000 0.33563 0.00000 0.00000 0.29636 0.00000 0.00000 3.50515 0.00000 0.00000 1.00000 0.00000 0.00000 + O3 0.22105 0.00000 0.00000 0.41215 0.00000 0.00000 0.50573 0.00000 0.00000 1.83513 0.00000 0.00000 1.00000 0.00000 0.00000 + N1 0.26340 0.00000 0.00000 0.62808 0.00000 0.00000 0.33048 0.00000 0.00000 2.07364 0.00000 0.00000 1.00000 0.00000 0.00000 + H1 0.12861 0.00000 0.00000 0.58669 0.00000 0.00000 0.41769 0.00000 0.00000 3.31527 0.00000 0.00000 1.00000 0.00000 0.00000 + H2 0.18953 0.00000 0.00000 0.71385 0.00000 0.00000 0.31124 0.00000 0.00000 4.46988 0.00000 0.00000 1.00000 0.00000 0.00000 + H3 0.43970 0.00000 0.00000 0.62023 0.00000 0.00000 0.34592 0.00000 0.00000 4.34151 0.00000 0.00000 1.00000 0.00000 0.00000 + C1 0.34384 0.00000 0.00000 0.44116 0.00000 0.00000 0.20155 0.00000 0.00000 1.73667 0.00000 0.00000 1.00000 0.00000 0.00000 + H11 0.55246 0.00000 0.00000 0.43345 0.00000 0.00000 0.24304 0.00000 0.00000 3.32279 0.00000 0.00000 1.00000 0.00000 0.00000 + H12 0.32537 0.00000 0.00000 0.38970 0.00000 0.00000 0.08264 0.00000 0.00000 3.05746 0.00000 0.00000 1.00000 0.00000 0.00000 + C2 0.20029 0.00000 0.00000 0.55716 0.00000 0.00000 0.18272 0.00000 0.00000 1.66017 0.00000 0.00000 1.00000 0.00000 0.00000 + H21 0.27650 0.00000 0.00000 0.60004 0.00000 0.00000 0.07688 0.00000 0.00000 2.15403 0.00000 0.00000 1.00000 0.00000 0.00000 + H22 -0.00383 0.00000 0.00000 0.54767 0.00000 0.00000 0.15762 0.00000 0.00000 4.71303 0.00000 0.00000 1.00000 0.00000 0.00000 + + ==> SCALE, EXTINCTION, CELL PARAMETERS FOR PATTERN# 1 + + => Scale factors ( 1: 6): + 2.711000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + + + => Extinction Parameters: + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 + + + => Lambda/2 param: + 0.000000 0.000000 0.000000 + + => Global user-weigthed Chi2 (Bragg contrib.): 24.4 + + => ---------> Pattern# 1 + => Phase: 1 + => RF2 -factor : 18.3 + => RF2w-factor : 12.5 + => RF -factor : 14.4 + => Chi2(Intens): 24.4 + => N_eff Reflect.: 171 with I > 3.00 sigma + + -------------------------------------------------------------------------------------------------------------------------------------------------------- + Pattern# 1 Phase No.: 1 Phase name: taurine + -------------------------------------------------------------------------------------------------------------------------------------------------------- + => F2cal= scale*Corr*F2 + h k l ivk cod F2obs F2cal F2cal(mag) Dif/sig Extinction(y) Sinthet/lamb Lambda/2-Contr RMsFx IMsFx RMsFy IMsFy RMsFz IMsFz RMiVx IMiVx RMiVy IMiVy RMiVz IMiVz + -4 10 -3 0 1 0.1000 1.2982 0.0000 0.0000 1.00000 Excl 0.61284 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -4 11 -4 0 1 3.4800 0.6770 0.0000 2.5026 1.00000 0.66801 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -4 11 -3 0 1 28.3500 19.9696 0.0000 3.4346 1.00000 0.64359 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -4 12 -4 0 1 12.8000 13.6741 0.0000 -0.5498 1.00000 0.69897 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -4 12 -3 0 1 19.8900 20.8403 0.0000 -0.4441 1.00000 0.67567 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -3 8 -3 0 1 23.7400 14.3027 0.0000 8.4262 1.00000 0.49349 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -3 9 -3 0 1 0.1700 0.4805 0.0000 0.0000 1.00000 Excl 0.52423 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + -3 10 -3 0 1 32.4900 31.0555 0.0000 0.9500 1.00000 0.55657 0.00000 0.00000 0.00000 0.00000 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0.00000 + 4 1 -6 0 1 1.4400 0.1503 0.0000 2.7441 1.00000 0.52270 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 4 1 -5 0 1 8.7800 16.4593 0.0000 -8.7264 1.00000 0.48128 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 2 -1 -4 0 1 1.2500 1.2388 0.0000 0.0934 1.00000 0.31082 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 3 -2 -7 0 1 6.7700 3.1199 0.0000 4.5626 1.00000 0.52076 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 3 -2 -6 0 1 26.0500 21.1275 0.0000 3.8159 1.00000 0.46966 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 3 2 -2 0 1 1.7400 1.1113 0.0000 2.2454 1.00000 0.31613 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 3 3 -2 0 1 331.0700 293.9396 0.0000 13.8546 1.00000 0.33036 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 4 4 -3 0 1 0.9300 2.0396 0.0000 0.0000 1.00000 Excl 0.44790 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 0 -1 0 0 0.0400 0.0000 0.0000 0.0000 1.00000 Excl 0.11079 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 2 0 -2 0 1 155.3200 155.5656 0.0000 -0.3189 1.00000 0.22158 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 3 -1 -3 0 1 15.8100 15.0869 0.0000 0.8035 1.00000 0.33513 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 3 0 -3 0 0 0.3200 0.0000 0.0000 0.0000 1.00000 Excl 0.33237 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 2 -3 -4 0 1 51.3800 29.3318 0.0000 18.8447 1.00000 0.33365 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 -1 -1 0 1 42.4900 41.8516 0.0000 2.6598 1.00000 0.11880 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 -4 -3 0 1 29.9200 20.2137 0.0000 11.2864 1.00000 0.26968 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 8 -2 0 1 113.9600 120.2537 0.0000 -6.1104 1.00000 0.37610 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 9 -2 0 1 14.5800 15.8607 0.0000 -2.2870 1.00000 0.41560 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 10 -2 0 1 6.0300 0.0017 0.0000 11.8202 1.00000 0.45573 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 11 -3 0 1 6.0100 3.9726 0.0000 3.4533 1.00000 0.51567 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 12 -3 0 1 0.3300 0.1524 0.0000 0.0000 1.00000 Excl 0.55519 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 13 -3 0 1 9.2700 0.8382 0.0000 7.8802 1.00000 0.59518 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 14 -3 0 1 0.6200 0.0030 0.0000 0.0000 1.00000 Excl 0.63554 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 15 -4 0 1 1.0400 0.3175 0.0000 0.0000 1.00000 Excl 0.69645 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + 1 15 -3 0 1 2.3700 0.2486 0.0000 0.0000 1.00000 Excl 0.67622 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 + + ----------------------------------------------------- + R-Factors and Chi2 for Integrated Intensity Pattern # 1 + ----------------------------------------------------- + => Phase: 1 + => RF2 -factor : 18.3 + => RF2w-factor : 12.5 + => RF -factor : 14.4 + => Chi2(Intens): 24.4 + => N_eff Reflect.: 171 with I > 3.00 sigma + + ----------------------------------------------------------------- + SYMBOLIC NAMES AND FINAL VALUES AND SIGMA OF REFINED PARAMETERS: + ----------------------------------------------------------------- + + + ------------------------------------------------------------------ + => Number of bytes for floating point variables: 4 + => Dimensions of dynamic allocated arrays in this run of FullProf: + ------------------------------------------------------------------ + + => Total approximate array memory (dynamic + static): 132451053 bytes + + MaxPOINT= 80000 Max.num. of points(+int. Inten.)/diffraction pattern + MaxREFLT= 25000 Max.num. of reflections/diffraction pattern + MaxPARAM= 500 Max.num. of refinable parameters + MaxOVERL= 9000 Max.num. of overlapping reflections + + ---------------------------------------------------------- + => Number of bytes for floating point arrays: 4 + => Dimensions of fixed arrays in this release of FullProf: + ---------------------------------------------------------- + + NPATT = 80 Max.num. of powder diffraction patterns + NATS = 830 Max.num. of atoms (all kind) in asymmetric unit + MPAR = 1800 Max.num. of non atomic parameters/phase + IEXCL = 30 Max.num. of excluded regions + IBACP = 377 Max.num. of background points for interpolation + NPHT = 16 Max.num. of phases + NMAGM = 8 Max.num. of rotation-matrices sets for magnetic structure + NBASIS = 12 Max.num. of basis functions associated to a single atom + NIREPS = 9 Max.num. of irreducible representations to be combined + N_EQ = 384 Max.num. of user-supplied symmetry operators/propagation vectors + NGL = 400 Max.num. of global parameters/diffraction pattern + N_LINC = 50 Max.num. of global linear restraints + NAT_P = 80 Max.num. of atomic parameters per atom + NCONST = 3500 Max.num. of slack constraints per phase + N_SPE = 30 Max.num. of different chemical species + N_FORM = 60 Max.num. of scattering factor values in a table + NPR = 150 Max.num. of points defining a numerical profile + INPR = 25 Max.num. of different numerical peak shapes + NPRC = 150 Max.num. of terms in the table for correcting intensities + NSOL = 10 Max.num. of solutions to be stored in Montecarlo searchs + + + CPU Time: 0.086 seconds + 0.001 minutes + + => Run finished at: Date: 24/06/2026 Time: 10:01:33.444 diff --git a/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.pcr b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.pcr new file mode 100644 index 000000000..96b1470c7 --- /dev/null +++ b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.pcr @@ -0,0 +1,73 @@ +COMM Taurine +! Current global Chi2 (Bragg contrib.) = 24.38 +! Files => DAT-file: taurine, PCR-file: taurine +!Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut + -1 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 +! +!Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 NLI Prf Ins Rpa Sym Hkl Fou Sho Ana + 0 0 1 0 1 0 4 0 0 3 0 -1 0 0 0 0 0 +! +!NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 + 20 0.10 1.00 1.00 1.00 1.00 0.1108 0.020000 150.0000 0.000 0.000 +! +! + 0 !Number of refined parameters +!------------------------------------------------------------------------------- +! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 18.3327 +!------------------------------------------------------------------------------- +taurine +! +!Nat Dis Ang Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More + 14 0 0 0.0 0.0 1.0 0 4 0 0 0 500.571 0 0 1 +! +!Jvi Jdi Hel Sol Mom Ter Brind RMua RMub RMuc Jtyp Nsp_Ref Ph_Shift N_Domains + 0 0 0 0 0 0 1.0000 1.0000 3.0000 0.0000 -1 0 0 0 +! +! +P 21/c <--Space group symbol +!Atom Typ X Y Z Biso Occ In Fin N_t Spc /Codes +S1 S 0.19448 0.35173 0.34730 1.37018 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +O1 O 0.31207 0.23951 0.35143 2.68011 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +O2 O -0.05909 0.33563 0.29636 3.50515 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +O3 O 0.22105 0.41215 0.50573 1.83513 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +N1 N 0.26340 0.62808 0.33048 2.07364 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +H1 H 0.12861 0.58669 0.41769 3.31527 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +H2 H 0.18953 0.71385 0.31124 4.46988 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +H3 H 0.43970 0.62023 0.34592 4.34151 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +C1 C 0.34384 0.44116 0.20155 1.73667 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +H11 H 0.55246 0.43345 0.24304 3.32279 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +H12 H 0.32537 0.38970 0.08264 3.05746 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +C2 C 0.20029 0.55716 0.18272 1.66017 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +H21 H 0.27650 0.60004 0.07688 2.15403 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +H22 H -0.00383 0.54767 0.15762 4.71303 1.00000 0 0 0 0 + 0.00 0.00 0.00 0.00 0.00 +!-------> Scale, Extinction and Cell Parameters for Pattern # 1 +! Scale Factors +! Sc1 Sc2 Sc3 Sc4 Sc5 Sc6 + 2.711 0.000 0.000 0.000 0.000 0.000 + 0.00 0.00 0.00 0.00 0.00 0.00 +! Extinction Parameters +! Ext1 Ext2 Ext3 Ext4 Ext5 Ext6 Ext7 Ext-Model + 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 +! a b c alpha beta gamma # Cell Info + 5.272901 11.656488 7.838297 90.000000 94.010994 90.000000 + 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 +! x-Lambda/2 + 0.00000 + 0.00 +! 2Th1/TOF1 2Th2/TOF2 Pattern to plot + 0.111 150.000 1 diff --git a/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.prf b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.prf new file mode 100644 index 000000000..65e99192e --- /dev/null +++ b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.prf @@ -0,0 +1,173 @@ + Taurine + Sinthet/lamb Gobs Gcal Sigma DIF/Sigma h k l iv Additional information + 0.11880 42.49 41.85 0.24 2.66 1 -1 -1 0 + 0.17474 4.09 4.31 0.08 -2.74 -1 3 -1 0 + 0.21243 14.44 15.06 0.17 -3.64 1 1 -3 0 + 0.22158 155.32 155.57 0.77 -0.32 2 0 -2 0 + 0.23611 38.08 39.08 0.32 -3.13 -1 2 -3 0 + 0.23761 3.54 3.58 0.10 -0.37 2 2 -2 0 + 0.24463 8.31 9.08 0.13 -5.91 1 3 -3 0 + 0.25152 36.82 40.54 0.34 -10.95 -2 2 -2 0 + 0.25485 0.84 1.00 0.05 -3.26 -1 3 -3 0 + 0.26657 1.06 0.84 0.06 3.64 1 0 -4 0 + 0.26919 8.31 8.52 0.18 -1.15 -2 3 -2 0 + 0.26968 29.92 20.21 0.86 11.29 1 -4 -3 0 + 0.27423 8.37 8.42 0.17 -0.29 2 2 -3 0 + 0.28004 22.33 22.90 0.24 -2.39 1 2 -4 0 + 0.29213 5.21 4.58 0.15 4.23 -2 4 -2 0 + 0.29225 3.53 3.92 0.15 -2.63 -2 2 -3 0 + 0.30723 42.16 43.92 0.39 -4.51 -1 5 -3 0 + 0.31082 1.25 1.24 0.12 0.09 2 -1 -4 0 + 0.31613 1.74 1.11 0.28 2.25 3 2 -2 0 + 0.32785 21.50 23.31 0.32 -5.65 -2 4 -3 0 + 0.33036 331.07 293.94 2.68 13.85 3 3 -2 0 + 0.33365 51.38 29.33 1.17 18.84 2 -3 -4 0 + 0.33365 27.22 29.33 0.37 -5.71 2 3 -4 0 + 0.33513 15.81 15.09 0.90 0.80 3 -1 -3 0 + 0.34327 91.22 84.02 1.32 5.46 3 2 -3 0 + 0.34948 0.57 1.07 0.09 -5.58 -2 6 -2 0 + 0.35153 30.31 29.40 0.38 2.39 1 3 -5 0 + 0.35641 9.58 5.46 0.45 9.16 3 3 -3 0 + 0.36952 8.50 10.28 0.51 -3.49 3 0 -4 0 + 0.37044 8.15 9.24 0.25 -4.35 2 2 -5 0 + 0.37200 3.10 0.89 0.30 7.38 3 1 -4 0 + 0.37610 113.96 120.25 1.03 -6.11 1 8 -2 0 + 0.37728 1.40 2.66 0.19 -6.66 -3 3 -3 0 + 0.37985 47.25 47.98 0.68 -1.08 -2 6 -3 0 + 0.39113 16.23 17.13 0.35 -2.57 1 1 -6 0 + 0.39116 59.75 59.63 0.58 0.21 1 5 -5 0 + 0.39315 13.25 12.31 0.28 3.35 0 2 -6 0 + 0.39913 3.73 1.55 0.21 10.39 2 4 -5 0 + 0.40427 3.15 2.10 0.20 5.26 -2 3 -5 0 + 0.40741 7.43 8.50 0.35 -3.06 3 4 -4 0 + 0.41013 119.53 119.35 1.20 0.15 -2 7 -3 0 + 0.41446 2.20 2.06 0.29 0.48 -3 5 -3 0 + 0.41560 14.58 15.86 0.56 -2.29 1 9 -2 0 + 0.41990 82.62 84.05 0.98 -1.46 -2 4 -5 0 + 0.42486 17.38 17.69 0.48 -0.66 2 2 -6 0 + 0.43555 0.75 0.07 0.14 4.83 2 3 -6 0 + 0.43820 65.48 60.67 1.28 3.76 -3 6 -3 0 + 0.43917 6.92 8.28 0.34 -4.00 -2 5 -5 0 + 0.44748 40.34 45.88 0.98 -5.65 3 4 -5 0 + 0.45573 6.03 0.00 0.51 11.82 1 10 -2 0 + 0.45914 3.14 2.81 0.25 1.34 1 2 -7 0 + 0.46164 11.93 8.61 0.48 6.93 -2 6 -5 0 + 0.46624 2.51 2.78 0.20 -1.36 1 6 -6 0 + 0.46813 14.14 14.06 0.48 0.17 2 5 -6 0 + 0.46966 26.05 21.13 1.29 3.82 3 -2 -6 0 + 0.46966 24.04 21.13 0.91 3.20 3 2 -6 0 + 0.47222 84.77 82.20 1.23 2.09 -2 4 -6 0 + 0.47243 35.11 35.33 1.03 -0.22 -3 6 -4 0 + 0.47513 1.00 0.56 0.18 2.45 -3 4 -5 0 + 0.47522 42.12 19.21 1.64 13.97 4 4 -4 0 + 0.47586 17.60 17.89 0.72 -0.41 2 1 -7 0 + 0.48128 8.78 16.46 0.88 -8.73 4 1 -5 0 + 0.48927 55.76 56.94 1.02 -1.16 2 6 -6 0 + 0.49007 7.01 11.52 0.72 -6.26 -4 3 -4 0 + 0.49349 23.74 14.30 1.12 8.43 -3 8 -3 0 + 0.49634 1.15 3.11 0.34 -5.75 4 3 -5 0 + 0.49710 0.88 1.28 0.24 -1.66 -3 7 -4 0 + 0.49945 3.10 4.48 0.25 -5.54 1 5 -7 0 + 0.50304 4.09 6.29 0.59 -3.73 -4 4 -4 0 + 0.50403 0.59 0.72 0.17 -0.76 2 4 -7 0 + 0.50914 86.71 85.63 1.64 0.66 3 5 -6 0 + 0.51442 0.66 2.02 0.21 -6.46 -2 8 -5 0 + 0.51567 6.01 3.97 0.59 3.45 1 11 -3 0 + 0.52076 6.77 3.12 0.80 4.56 3 -2 -7 0 + 0.52086 18.78 12.83 0.75 7.93 1 2 -8 0 + 0.52093 54.06 34.53 2.27 8.61 4 0 -6 0 + 0.52270 1.44 0.15 0.47 2.74 4 1 -6 0 + 0.52750 9.09 6.57 0.48 5.25 0 3 -8 0 + 0.52952 3.23 1.42 0.44 4.10 3 3 -7 0 + 0.53079 3.35 9.26 0.69 -8.57 -4 7 -3 0 + 0.53522 9.48 15.50 0.68 -8.85 -3 7 -5 0 + 0.53837 1.93 0.82 0.47 2.36 -4 6 -4 0 + 0.53930 11.41 13.58 0.63 -3.44 2 6 -7 0 + 0.54185 5.92 2.67 0.43 7.57 1 7 -7 0 + 0.54398 12.16 5.51 0.75 8.87 -2 9 -5 0 + 0.54846 33.47 13.21 1.68 12.06 4 4 -6 0 + 0.55657 32.49 31.06 1.51 0.95 -3 10 -3 0 + 0.55672 2.85 2.63 0.34 0.66 1 5 -8 0 + 0.56007 16.49 14.18 0.80 2.88 2 4 -8 0 + 0.56015 1.76 4.45 0.49 -5.48 -4 7 -4 0 + 0.56336 104.92 66.51 2.66 14.44 4 5 -6 0 + 0.56675 1.12 1.25 0.23 -0.57 1 8 -7 0 + 0.57314 24.90 23.99 1.54 0.59 4 2 -7 0 + 0.57444 3.90 2.36 0.61 2.53 3 2 -8 0 + 0.57452 5.50 11.71 0.61 -10.17 3 6 -7 0 + 0.57461 4.77 6.36 0.45 -3.53 1 6 -8 0 + 0.57466 1.71 1.84 0.31 -0.43 2 5 -8 0 + 0.58239 22.09 19.42 1.25 2.14 3 3 -8 0 + 0.58306 5.81 6.41 0.54 -1.11 1 2 -9 0 + 0.58449 17.52 22.52 1.55 -3.23 -4 4 -6 0 + 0.58973 7.44 4.04 0.60 5.67 0 3 -9 0 + 0.59489 1.28 0.30 0.35 2.81 2 1 -9 0 + 0.59518 9.27 0.84 1.07 7.88 1 13 -3 0 + 0.59849 3.14 8.50 0.67 -8.00 -4 5 -6 0 + 0.61530 3.22 0.01 0.48 6.70 1 5 -9 0 + 0.61549 11.08 13.50 1.53 -1.58 -5 4 -5 0 + 0.61668 4.44 8.49 0.75 -5.41 -3 10 -5 0 + 0.61717 9.55 2.61 1.24 5.60 4 1 -8 0 + 0.61765 3.00 2.99 0.50 0.03 2 4 -9 0 + 0.61781 6.75 8.43 0.67 -2.50 1 8 -8 0 + 0.62564 23.49 22.18 1.72 0.76 3 -1 -9 0 + 0.62899 34.65 46.14 2.04 -5.63 4 3 -8 0 + 0.63091 2.32 2.87 0.48 -1.15 2 5 -9 0 + 0.63154 3.67 3.16 0.54 0.94 1 6 -9 0 + 0.63729 2.02 2.29 0.60 -0.44 3 3 -9 0 + 0.63987 17.81 23.84 1.21 -4.99 -3 5 -8 0 + 0.64263 4.97 1.45 0.58 6.07 1 9 -8 0 + 0.64359 28.35 19.97 2.44 3.43 -4 11 -3 0 + 0.64513 13.45 5.15 1.13 7.35 -2 11 -6 0 + 0.64725 14.38 14.32 1.29 0.04 -3 11 -5 0 + 0.64732 3.12 4.99 0.72 -2.59 3 4 -9 0 + 0.65020 15.10 12.21 1.03 2.81 1 7 -9 0 + 0.65549 5.44 2.77 0.80 3.34 -3 6 -8 0 + 0.65570 2.63 4.21 0.87 -1.82 -4 8 -6 0 + 0.66679 4.67 3.07 1.21 1.32 -5 5 -6 0 + 0.66801 3.48 0.68 1.12 2.50 -4 11 -4 0 + 0.67271 4.37 4.94 0.96 -0.60 4 2 -9 0 + 0.67567 19.89 20.84 2.14 -0.44 -4 12 -3 0 + 0.67916 7.44 2.11 1.11 4.80 -3 12 -5 0 + 0.68025 11.50 13.14 1.49 -1.10 5 6 -7 0 + 0.68851 11.45 11.15 1.12 0.27 2 5 -10 0 + 0.69368 4.04 8.82 0.80 -5.97 -3 8 -8 0 + 0.69400 11.63 12.14 1.09 -0.46 1 9 -9 0 + 0.69897 12.80 13.67 1.59 -0.55 -4 12 -4 0 + 0.70305 19.59 12.78 1.55 4.39 2 6 -10 0 + 0.70833 19.49 23.44 1.60 -2.47 -3 6 -9 0 + 0.71587 2.98 1.27 0.77 2.22 -3 9 -8 0 + 0.71650 3.39 4.34 0.77 -1.24 -2 12 -7 0 + 0.71957 8.83 10.07 1.35 -0.92 -4 9 -7 0 + 0.72099 6.56 1.29 1.30 4.05 5 6 -8 0 + 0.73033 4.49 0.42 1.39 2.93 -5 10 -5 0 + 0.73167 23.28 9.67 2.05 6.64 4 7 -9 0 + 0.73390 3.41 5.03 0.77 -2.11 3 9 -9 0 + 0.74525 11.30 7.69 1.61 2.24 3 2 -11 0 + 0.75029 5.59 3.89 1.16 1.47 4 8 -9 0 + 0.75340 4.81 8.48 1.34 -2.74 -5 5 -8 0 + 0.75970 5.45 2.24 1.23 2.61 -4 12 -6 0 + 0.76320 33.36 18.95 2.40 6.00 3 8 -10 0 + 0.76460 7.29 9.16 1.28 -1.46 1 7 -11 0 + 0.76671 9.61 6.42 1.95 1.64 -5 6 -8 0 + 0.77237 7.95 6.59 1.49 0.91 -4 7 -9 0 + 0.78233 2.01 0.71 0.60 2.17 2 10 -10 0 + 0.78376 4.11 3.27 1.06 0.80 3 6 -11 0 + 0.78708 3.78 3.16 0.97 0.64 -3 10 -9 0 + 0.78811 6.09 1.15 1.16 4.26 2 3 -12 0 + 0.79459 13.39 16.97 1.86 -1.92 4 4 -11 0 + 0.79971 16.05 18.84 2.24 -1.24 3 0 -12 0 + 0.80430 5.13 4.00 1.26 0.89 3 2 -12 0 + 0.80543 5.07 7.95 1.05 -2.75 3 10 -10 0 + 0.81340 7.76 4.96 1.66 1.69 -5 6 -9 0 + 0.81742 6.48 7.56 1.50 -0.72 4 6 -11 0 + 0.82320 5.48 9.78 1.49 -2.89 -4 7 -10 0 + 0.82797 11.85 14.76 1.78 -1.64 3 5 -12 0 + 0.83439 6.98 6.92 1.37 0.04 2 10 -11 0 + 0.83989 5.74 4.30 1.32 1.09 1 8 -12 0 + 0.84011 7.84 4.47 1.55 2.17 3 6 -12 0 + 0.84407 10.01 5.70 1.72 2.50 2 2 -13 0 + 0.85092 9.11 1.46 2.06 3.71 -3 14 -8 0 + 0.85384 5.35 6.23 1.45 -0.61 -4 11 -9 0 + 0.85831 3.75 3.07 1.15 0.59 1 9 -12 0 + 0.85852 5.13 4.90 1.37 0.17 0 5 -13 0 diff --git a/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.sum b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.sum new file mode 100644 index 000000000..a3a692d85 --- /dev/null +++ b/docs/docs/verification/fullprof/sc-neut-tof_taurine_basic/taurine.sum @@ -0,0 +1,98 @@ + + + ********************************************************** + ** 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: 24/06/2026 Time: 10:01:33.360 + + => PCR file code: taurine + => DAT file code: taurine -> Relative contribution: 1.0000 + => Title: Taurine + + ==> CONDITIONS OF THIS RUN FOR PATTERN No.: 1 + + => Refinement/Calculation of Neutron integrated intensity(Laue or monochromatic) data or Flipping Ratios + => Neutron Time-Of-Flight data + =>-------> Pattern# 1 + => Integrated intensities or Flipping Ratios as observations for phase: 1 + => Crystal Structure Refinement for phase: 1 + => The density (volumic mass) of phase 1 is: 1.730 g/cm3 + + ==> RESULTS OF REFINEMENT: + + + => No. of fitted parameters: 0 + + +------------------------------------------------------------------------------ + => Phase No. 1 taurine P 21/c +------------------------------------------------------------------------------ + + => No. of reflections for pattern#: 1: 171 + + + ==> ATOM PARAMETERS: + + Name x sx y sy z sz B sB occ. socc. Mult + S1 0.19448( 0) 0.35173( 0) 0.34730( 0) 1.370( 0) 1.000( 0) 4 + O1 0.31207( 0) 0.23951( 0) 0.35143( 0) 2.680( 0) 1.000( 0) 4 + O2 -0.05909( 0) 0.33563( 0) 0.29636( 0) 3.505( 0) 1.000( 0) 4 + O3 0.22105( 0) 0.41215( 0) 0.50573( 0) 1.835( 0) 1.000( 0) 4 + N1 0.26340( 0) 0.62808( 0) 0.33048( 0) 2.074( 0) 1.000( 0) 4 + H1 0.12861( 0) 0.58669( 0) 0.41769( 0) 3.315( 0) 1.000( 0) 4 + H2 0.18953( 0) 0.71385( 0) 0.31124( 0) 4.470( 0) 1.000( 0) 4 + H3 0.43970( 0) 0.62023( 0) 0.34592( 0) 4.342( 0) 1.000( 0) 4 + C1 0.34384( 0) 0.44116( 0) 0.20155( 0) 1.737( 0) 1.000( 0) 4 + H11 0.55246( 0) 0.43345( 0) 0.24304( 0) 3.323( 0) 1.000( 0) 4 + H12 0.32537( 0) 0.38970( 0) 0.08264( 0) 3.057( 0) 1.000( 0) 4 + C2 0.20029( 0) 0.55716( 0) 0.18272( 0) 1.660( 0) 1.000( 0) 4 + H21 0.27650( 0) 0.60004( 0) 0.07688( 0) 2.154( 0) 1.000( 0) 4 + H22 -0.00383( 0) 0.54767( 0) 0.15762( 0) 4.713( 0) 1.000( 0) 4 + + ==> SCALE, EXTINCTION, CELL PARAMETERS FOR PATTERN# 1 + + ==> OVERALL PARAMETERS: + + + + => Scale factors ( 1: 6): + 2.711000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + + + => Extinction parameters: + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + 0.000000 0.000000 + + + => Global user-weigthed Chi2 (Bragg contrib.): 24.4 + + ----------------------------------------------------- + R-Factors and Chi2 for Integrated Intensity Pattern # 1 + ----------------------------------------------------- + => Phase: 1 + => RF2 -factor : 18.3 + => RF2w-factor : 12.5 + => RF -factor : 14.4 + => Chi2(Intens): 24.4 + => N_eff Reflect.: 171 with I > 3.00 sigma + + + CPU Time: 0.086 seconds + 0.001 minutes + + => Run finished at: Date: 24/06/2026 Time: 10:01:33.444 diff --git a/docs/docs/verification/index.md b/docs/docs/verification/index.md index e9623182a..f8829e66b 100644 --- a/docs/docs/verification/index.md +++ b/docs/docs/verification/index.md @@ -83,6 +83,13 @@ term); these are marked below and inside the notebook. Jorgensen-Von Dreele profile (`size_g`/`strain_g`, `size_l`/`strain_l`). +### Diamond structure + +- [pd-neut-tof Diamond DREAM](pd-neut-tof_diamond_dream.ipynb) – + **Jorgensen (back-to-back exponentials ⊗ Gaussian)** profile fitted to + **McStas-simulated reduced data from the DREAM diffractometer at ESS** + (scale-only adjustment between cryspy and FullProf). + ## Powder, X-Ray, Constant Wavelength ### LiF structure @@ -105,22 +112,29 @@ term); these are marked below and inside the notebook. anglesite X-ray round-robin case (**Pseudo-Voigt + Bérar-Baldinozzi asymmetry**). -## Single Crystal, Neutron, Constant Wavelength +## Single Crystal ### Pr2NiO4 structure - [sc-neut-cwl Pr2NiO4 basic](sc-neut-cwl_Pr2NiO4_basic.ipynb) – - calculated F² with **anisotropic β-tensor ADPs**. + **neutron, constant wavelength**; **anisotropic β-tensor ADPs**. ### Tb2Ti2O7 structure - [sc-neut-cwl Tb2Ti2O7 basic](sc-neut-cwl_Tb2Ti2O7_basic.ipynb) – - baseline with **isotropic ADPs**. + **neutron, constant wavelength**; baseline with **isotropic ADPs**. - [sc-neut-cwl Tb2Ti2O7 isotropic extinction](sc-neut-cwl_Tb2Ti2O7_isotropic-extinction.ipynb) - – **isotropic Becker-Coppens extinction** (Gaussian model). _Known - difference: cryspy and FullProf use different extinction conventions._ + – **neutron, constant wavelength**; **isotropic Becker-Coppens + extinction** (Gaussian model). _Known difference: cryspy and FullProf + use different extinction conventions._ - [sc-neut-cwl Tb2Ti2O7 anisotropic β ADPs](sc-neut-cwl_Tb2Ti2O7_anisotropic-adp.ipynb) - – **anisotropic β-tensor ADPs**. + – **neutron, constant wavelength**; **anisotropic β-tensor ADPs**. + +### Taurine structure + +- [sc-neut-tof Taurine basic](sc-neut-tof_taurine_basic.ipynb) – + **neutron, time-of-flight**; **isotropic ADPs** (without extinction + correction). ## Powder, Total Scattering (Pair Distribution Function) diff --git a/docs/docs/verification/pd-neut-tof_diamond_dream.ipynb b/docs/docs/verification/pd-neut-tof_diamond_dream.ipynb new file mode 100644 index 000000000..4c426cf2f --- /dev/null +++ b/docs/docs/verification/pd-neut-tof_diamond_dream.ipynb @@ -0,0 +1,295 @@ +{ + "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": [ + "# Diamond — powder neutron TOF — DREAM (ESS, McStas)\n", + "\n", + "Verifies the Jorgensen back-to-back exponential TOF profile against a\n", + "FullProf reference fitted to McStas-simulated reduced data from the\n", + "DREAM diffractometer at ESS.\n", + "\n", + "**Refinement:** the overall scale only; all other parameters are\n", + "taken from the FullProf reference." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "import easydiffraction as edi\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 = edi.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='diamond')\n", + "\n", + "structure.space_group.name_h_m = 'F d -3 m' # FullProf Space group symbol\n", + "structure.space_group.coord_system_code = '1' # FullProf \":1\" origin choice\n", + "\n", + "structure.cell.length_a = 3.567 # FullProf a\n", + "\n", + "structure.atom_sites.create(\n", + " id='C', # FullProf Atom\n", + " type_symbol='C', # FullProf Typ\n", + " fract_x=0.125, # FullProf X\n", + " fract_y=0.125, # FullProf Y\n", + " fract_z=0.125, # FullProf Z\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=0.89263, # 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-tof_diamond_dream'\n", + "FULLPROF_PRF_FILE = 'diamond.prf'\n", + "FULLPROF_SUM_FILE = 'diamond.sum'\n", + "FULLPROF_BAC_FILE = 'diamond.bac'\n", + "FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE)\n", + "\n", + "FULLPROF_ZERO = 0.0 # FullProf Zero\n", + "FULLPROF_SCALE = 0.1011780 # FullProf Scale\n", + "FULLPROF_TWOTHETA_BANK = 90.0 # FullProf 2ThetaBank\n", + "FULLPROF_DTT1 = 28385.86133 # FullProf Dtt1\n", + "FULLPROF_DTT2 = 0.0 # FullProf Dtt2\n", + "FULLPROF_SIGMA_0 = 46937.7188 # FullProf Sigma-0\n", + "FULLPROF_SIGMA_1 = 4887.9180 # FullProf Sigma-1\n", + "FULLPROF_SIGMA_2 = 0.0 # FullProf Sigma-2\n", + "FULLPROF_ALPHA_0 = 0.0 # FullProf alph0\n", + "FULLPROF_ALPHA_1 = 0.022544 # FullProf alph1\n", + "FULLPROF_BETA_0 = 0.014330 # FullProf beta0\n", + "FULLPROF_BETA_1 = 0.0 # FullProf beta1\n", + "FULLPROF_WDT = 30.0 # FullProf Wdt\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='diamond',\n", + " sample_form='powder',\n", + " beam_mode='time-of-flight',\n", + " radiation_probe='neutron',\n", + " scattering_type='bragg',\n", + ")\n", + "verify.set_reference_as_measured(experiment, x, calc_fullprof)\n", + "\n", + "experiment.linked_structures.create(structure_id='diamond', scale=FULLPROF_SCALE)\n", + "\n", + "experiment.instrument.setup_twotheta_bank = FULLPROF_TWOTHETA_BANK\n", + "experiment.instrument.calib_d_to_tof_offset = FULLPROF_ZERO\n", + "experiment.instrument.calib_d_to_tof_linear = FULLPROF_DTT1\n", + "experiment.instrument.calib_d_to_tof_quadratic = FULLPROF_DTT2\n", + "\n", + "experiment.peak.type = 'jorgensen'\n", + "experiment.peak.broad_gauss_sigma_0 = FULLPROF_SIGMA_0\n", + "experiment.peak.broad_gauss_sigma_1 = FULLPROF_SIGMA_1\n", + "experiment.peak.broad_gauss_sigma_2 = FULLPROF_SIGMA_2\n", + "experiment.peak.rise_alpha_0 = FULLPROF_ALPHA_0\n", + "experiment.peak.rise_alpha_1 = FULLPROF_ALPHA_1\n", + "experiment.peak.decay_beta_0 = FULLPROF_BETA_0\n", + "experiment.peak.decay_beta_1 = FULLPROF_BETA_1\n", + "\n", + "experiment.excluded_regions.create(id='1', start=0, end=10000)\n", + "experiment.excluded_regions.create(id='2', start=70000, end=200000)\n", + "\n", + "experiment.peak.cutoff_fwhm = FULLPROF_WDT\n", + "\n", + "project.experiments.add(experiment)" + ] + }, + { + "cell_type": "markdown", + "id": "11", + "metadata": {}, + "source": [ + "## edi-cryspy VS FullProf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "12", + "metadata": {}, + "outputs": [], + "source": [ + "experiment.calculator.type = 'cryspy'\n", + "\n", + "experiment.linked_structures['diamond'].scale = FULLPROF_SCALE\n", + "\n", + "project.analysis.calculate()\n", + "calc_ed_cryspy = experiment.data.intensity_calc\n", + "LABEL_ED_CRYSPY = verify.engine_label('cryspy')\n", + "\n", + "project.display.pattern_comparison(\n", + " 'diamond',\n", + " reference=calc_fullprof,\n", + " candidate=calc_ed_cryspy,\n", + " reference_label=FULLPROF_LABEL,\n", + " candidate_label=LABEL_ED_CRYSPY,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "13", + "metadata": {}, + "source": [ + "## Fit edi-cryspy to FullProf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "14", + "metadata": {}, + "outputs": [], + "source": [ + "experiment.linked_structures['diamond'].scale.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", + "LABEL_ED_CRYSPY_REFINED = verify.engine_label('cryspy', note='refined')\n", + "\n", + "project.display.pattern_comparison(\n", + " 'diamond',\n", + " reference=calc_fullprof,\n", + " candidate=calc_ed_cryspy_refined,\n", + " reference_label=FULLPROF_LABEL,\n", + " candidate_label=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", + " (\n", + " f'{LABEL_ED_CRYSPY_REFINED} vs {FULLPROF_LABEL}',\n", + " verify.restrict_to_included(experiment, calc_fullprof),\n", + " calc_ed_cryspy_refined,\n", + " ),\n", + " ],\n", + ")" + ] + } + ], + "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-tof_diamond_dream.py b/docs/docs/verification/pd-neut-tof_diamond_dream.py new file mode 100644 index 000000000..a22c48ebd --- /dev/null +++ b/docs/docs/verification/pd-neut-tof_diamond_dream.py @@ -0,0 +1,166 @@ +# %% [markdown] +# # Diamond — powder neutron TOF — DREAM (ESS, McStas) +# +# Verifies the Jorgensen back-to-back exponential TOF profile against a +# FullProf reference fitted to McStas-simulated reduced data from the +# DREAM diffractometer at ESS. +# +# **Refinement:** the overall scale only; all other parameters are +# taken from the FullProf reference. + +# %% +import easydiffraction as edi +from easydiffraction import ExperimentFactory +from easydiffraction import StructureFactory +from easydiffraction.analysis import verification as verify + +# %% [markdown] +# ## Build the project + +# %% +project = edi.Project() + +# %% [markdown] +# ## Define the structure + +# %% +structure = StructureFactory.from_scratch(name='diamond') + +structure.space_group.name_h_m = 'F d -3 m' # FullProf Space group symbol +structure.space_group.coord_system_code = '1' # FullProf ":1" origin choice + +structure.cell.length_a = 3.567 # FullProf a + +structure.atom_sites.create( + id='C', # FullProf Atom + type_symbol='C', # FullProf Typ + fract_x=0.125, # FullProf X + fract_y=0.125, # FullProf Y + fract_z=0.125, # FullProf Z + adp_type='Biso', # FullProf Biso + adp_iso=0.89263, # FullProf Biso +) + +project.structures.add(structure) + +# %% [markdown] +# ## Load the FullProf reference + +# %% +FULLPROF_PROJECT_DIR = 'pd-neut-tof_diamond_dream' +FULLPROF_PRF_FILE = 'diamond.prf' +FULLPROF_SUM_FILE = 'diamond.sum' +FULLPROF_BAC_FILE = 'diamond.bac' +FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE) + +FULLPROF_ZERO = 0.0 # FullProf Zero +FULLPROF_SCALE = 0.1011780 # FullProf Scale +FULLPROF_TWOTHETA_BANK = 90.0 # FullProf 2ThetaBank +FULLPROF_DTT1 = 28385.86133 # FullProf Dtt1 +FULLPROF_DTT2 = 0.0 # FullProf Dtt2 +FULLPROF_SIGMA_0 = 46937.7188 # FullProf Sigma-0 +FULLPROF_SIGMA_1 = 4887.9180 # FullProf Sigma-1 +FULLPROF_SIGMA_2 = 0.0 # FullProf Sigma-2 +FULLPROF_ALPHA_0 = 0.0 # FullProf alph0 +FULLPROF_ALPHA_1 = 0.022544 # FullProf alph1 +FULLPROF_BETA_0 = 0.014330 # FullProf beta0 +FULLPROF_BETA_1 = 0.0 # FullProf beta1 +FULLPROF_WDT = 30.0 # FullProf Wdt + +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='diamond', + sample_form='powder', + beam_mode='time-of-flight', + radiation_probe='neutron', + scattering_type='bragg', +) +verify.set_reference_as_measured(experiment, x, calc_fullprof) + +experiment.linked_structures.create(structure_id='diamond', scale=FULLPROF_SCALE) + +experiment.instrument.setup_twotheta_bank = FULLPROF_TWOTHETA_BANK +experiment.instrument.calib_d_to_tof_offset = FULLPROF_ZERO +experiment.instrument.calib_d_to_tof_linear = FULLPROF_DTT1 +experiment.instrument.calib_d_to_tof_quadratic = FULLPROF_DTT2 + +experiment.peak.type = 'jorgensen' +experiment.peak.broad_gauss_sigma_0 = FULLPROF_SIGMA_0 +experiment.peak.broad_gauss_sigma_1 = FULLPROF_SIGMA_1 +experiment.peak.broad_gauss_sigma_2 = FULLPROF_SIGMA_2 +experiment.peak.rise_alpha_0 = FULLPROF_ALPHA_0 +experiment.peak.rise_alpha_1 = FULLPROF_ALPHA_1 +experiment.peak.decay_beta_0 = FULLPROF_BETA_0 +experiment.peak.decay_beta_1 = FULLPROF_BETA_1 + +experiment.excluded_regions.create(id='1', start=0, end=10000) +experiment.excluded_regions.create(id='2', start=70000, end=200000) + +experiment.peak.cutoff_fwhm = FULLPROF_WDT + +project.experiments.add(experiment) + +# %% [markdown] +# ## edi-cryspy VS FullProf + +# %% +experiment.calculator.type = 'cryspy' + +experiment.linked_structures['diamond'].scale = FULLPROF_SCALE + +project.analysis.calculate() +calc_ed_cryspy = experiment.data.intensity_calc +LABEL_ED_CRYSPY = verify.engine_label('cryspy') + +project.display.pattern_comparison( + 'diamond', + reference=calc_fullprof, + candidate=calc_ed_cryspy, + reference_label=FULLPROF_LABEL, + candidate_label=LABEL_ED_CRYSPY, +) + +# %% [markdown] +# ## Fit edi-cryspy to FullProf + +# %% +experiment.linked_structures['diamond'].scale.free = True + +project.analysis.fit() +project.display.fit.results() + +project.analysis.calculate() +calc_ed_cryspy_refined = experiment.data.intensity_calc +LABEL_ED_CRYSPY_REFINED = verify.engine_label('cryspy', note='refined') + +project.display.pattern_comparison( + 'diamond', + reference=calc_fullprof, + candidate=calc_ed_cryspy_refined, + reference_label=FULLPROF_LABEL, + candidate_label=LABEL_ED_CRYSPY_REFINED, +) + +# %% [markdown] +# ## Agreement check + +# %% +verify.assert_patterns_agree( + [ + ( + f'{LABEL_ED_CRYSPY_REFINED} vs {FULLPROF_LABEL}', + verify.restrict_to_included(experiment, calc_fullprof), + calc_ed_cryspy_refined, + ), + ], +) diff --git a/docs/docs/verification/sc-neut-tof_taurine_basic.ipynb b/docs/docs/verification/sc-neut-tof_taurine_basic.ipynb new file mode 100644 index 000000000..9cc03c3f4 --- /dev/null +++ b/docs/docs/verification/sc-neut-tof_taurine_basic.ipynb @@ -0,0 +1,289 @@ +{ + "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": [ + "# Taurine - single-crystal neutron TOF - basic\n", + "\n", + "Verifies calculated F2 values for a no-extinction neutron\n", + "single-crystal time-of-flight baseline with isotropic ADPs.\n", + "\n", + "**Refinement:** the overall scale only; all other parameters are\n", + "taken from the FullProf reference. Extinction is set to zero in the\n", + "FullProf model so the comparison focuses on the structure-factor\n", + "physics shared by cryspy and FullProf." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2", + "metadata": {}, + "outputs": [], + "source": [ + "import easydiffraction as edi\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 = edi.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='taurine')\n", + "\n", + "structure.space_group.name_h_m = 'P 21/c' # FullProf Space group symbol\n", + "\n", + "structure.cell.length_a = 5.272901 # FullProf a\n", + "structure.cell.length_b = 11.656488 # FullProf b\n", + "structure.cell.length_c = 7.838297 # FullProf c\n", + "structure.cell.angle_beta = 94.010994 # FullProf beta\n", + "\n", + "# fmt: off\n", + "_ATOMS = [\n", + " ('S1', 'S', 0.19448, 0.35173, 0.34730, 1.37018),\n", + " ('O1', 'O', 0.31207, 0.23951, 0.35143, 2.68011),\n", + " ('O2', 'O', -0.05909, 0.33563, 0.29636, 3.50515),\n", + " ('O3', 'O', 0.22105, 0.41215, 0.50573, 1.83513),\n", + " ('N1', 'N', 0.26340, 0.62808, 0.33048, 2.07364),\n", + " ('H1', 'H', 0.12861, 0.58669, 0.41769, 3.31527),\n", + " ('H2', 'H', 0.18953, 0.71385, 0.31124, 4.46988),\n", + " ('H3', 'H', 0.43970, 0.62023, 0.34592, 4.34151),\n", + " ('C1', 'C', 0.34384, 0.44116, 0.20155, 1.73667),\n", + " ('H11', 'H', 0.55246, 0.43345, 0.24304, 3.32279),\n", + " ('H12', 'H', 0.32537, 0.38970, 0.08264, 3.05746),\n", + " ('C2', 'C', 0.20029, 0.55716, 0.18272, 1.66017),\n", + " ('H21', 'H', 0.27650, 0.60004, 0.07688, 2.15403),\n", + " ('H22', 'H', -0.00383, 0.54767, 0.15762, 4.71303),\n", + "]\n", + "# fmt: on\n", + "\n", + "for _id, _type, _x, _y, _z, _biso in _ATOMS:\n", + " structure.atom_sites.create(\n", + " id=_id, # FullProf Atom\n", + " type_symbol=_type, # FullProf Typ\n", + " fract_x=_x, # FullProf X\n", + " fract_y=_y, # FullProf Y\n", + " fract_z=_z, # FullProf Z\n", + " adp_type='Biso', # FullProf Biso\n", + " adp_iso=_biso, # FullProf Biso\n", + " )\n", + "\n", + "project.structures.add(structure)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7", + "metadata": {}, + "outputs": [], + "source": [ + "structure.show_as_text()" + ] + }, + { + "cell_type": "markdown", + "id": "8", + "metadata": {}, + "source": [ + "## Load the FullProf reference" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9", + "metadata": {}, + "outputs": [], + "source": [ + "FULLPROF_PROJECT_DIR = 'sc-neut-tof_taurine_basic'\n", + "FULLPROF_OUT_FILE = 'taurine.out'\n", + "FULLPROF_SCALE = 2.711 # FullProf Scale\n", + "\n", + "f2calc = verify.load_fullprof_sc_f2calc(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE)\n", + "FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE)" + ] + }, + { + "cell_type": "markdown", + "id": "10", + "metadata": {}, + "source": [ + "## Create the experiment" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "11", + "metadata": {}, + "outputs": [], + "source": [ + "experiment = ExperimentFactory.from_scratch(\n", + " name='taurine',\n", + " sample_form='single crystal',\n", + " beam_mode='time-of-flight',\n", + " radiation_probe='neutron',\n", + " scattering_type='bragg',\n", + ")\n", + "\n", + "experiment.linked_structure.structure_id = 'taurine'\n", + "experiment.linked_structure.scale = FULLPROF_SCALE\n", + "\n", + "verify.set_reference_reflections(experiment, f2calc)\n", + "\n", + "project.experiments.add(experiment)" + ] + }, + { + "cell_type": "markdown", + "id": "12", + "metadata": {}, + "source": [ + "## edi-cryspy VS FullProf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "13", + "metadata": {}, + "outputs": [], + "source": [ + "calc_ed_cryspy = verify.calculate_reflections(project, experiment, 'cryspy')\n", + "LABEL_ED_CRYSPY = verify.engine_label('cryspy')\n", + "reference, candidate = verify.align_reflections(f2calc, calc_ed_cryspy)\n", + "\n", + "project.display.reflection_comparison(\n", + " 'taurine',\n", + " reference=reference,\n", + " candidate=candidate,\n", + " reference_label=FULLPROF_LABEL,\n", + " candidate_label=LABEL_ED_CRYSPY,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "14", + "metadata": {}, + "source": [ + "## Fit edi-cryspy to FullProf" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15", + "metadata": {}, + "outputs": [], + "source": [ + "experiment.calculator.type = 'cryspy'\n", + "\n", + "experiment.linked_structure.scale.free = True\n", + "\n", + "project.analysis.fit()\n", + "project.display.fit.results()\n", + "\n", + "calc_ed_cryspy_refined = verify.calculate_reflections(project, experiment, 'cryspy')\n", + "LABEL_ED_CRYSPY_REFINED = verify.engine_label('cryspy', note='scale only')\n", + "reference_refined, candidate_refined = verify.align_reflections(f2calc, calc_ed_cryspy_refined)\n", + "\n", + "project.display.reflection_comparison(\n", + " 'taurine',\n", + " reference=reference_refined,\n", + " candidate=candidate_refined,\n", + " reference_label=FULLPROF_LABEL,\n", + " candidate_label=LABEL_ED_CRYSPY_REFINED,\n", + ")\n", + "\n", + "verify.report_refinement_closeness(\n", + " reference,\n", + " candidate,\n", + " candidate_refined,\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "16", + "metadata": {}, + "source": [ + "## Agreement check" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "17", + "metadata": {}, + "outputs": [], + "source": [ + "verify.assert_patterns_agree([\n", + " (f'{LABEL_ED_CRYSPY_REFINED} vs {FULLPROF_LABEL}', reference_refined, candidate_refined),\n", + "])" + ] + } + ], + "metadata": { + "jupytext": { + "cell_metadata_filter": "-all", + "main_language": "python", + "notebook_metadata_filter": "-all" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/docs/docs/verification/sc-neut-tof_taurine_basic.py b/docs/docs/verification/sc-neut-tof_taurine_basic.py new file mode 100644 index 000000000..9a28ca9cf --- /dev/null +++ b/docs/docs/verification/sc-neut-tof_taurine_basic.py @@ -0,0 +1,153 @@ +# %% [markdown] +# # Taurine - single-crystal neutron TOF - basic +# +# Verifies calculated F2 values for a no-extinction neutron +# single-crystal time-of-flight baseline with isotropic ADPs. +# +# **Refinement:** the overall scale only; all other parameters are +# taken from the FullProf reference. Extinction is set to zero in the +# FullProf model so the comparison focuses on the structure-factor +# physics shared by cryspy and FullProf. + +# %% +import easydiffraction as edi +from easydiffraction import ExperimentFactory +from easydiffraction import StructureFactory +from easydiffraction.analysis import verification as verify + +# %% [markdown] +# ## Build the project + +# %% +project = edi.Project() + +# %% [markdown] +# ## Define the structure + +# %% +structure = StructureFactory.from_scratch(name='taurine') + +structure.space_group.name_h_m = 'P 21/c' # FullProf Space group symbol + +structure.cell.length_a = 5.272901 # FullProf a +structure.cell.length_b = 11.656488 # FullProf b +structure.cell.length_c = 7.838297 # FullProf c +structure.cell.angle_beta = 94.010994 # FullProf beta + +# fmt: off +_ATOMS = [ + ('S1', 'S', 0.19448, 0.35173, 0.34730, 1.37018), + ('O1', 'O', 0.31207, 0.23951, 0.35143, 2.68011), + ('O2', 'O', -0.05909, 0.33563, 0.29636, 3.50515), + ('O3', 'O', 0.22105, 0.41215, 0.50573, 1.83513), + ('N1', 'N', 0.26340, 0.62808, 0.33048, 2.07364), + ('H1', 'H', 0.12861, 0.58669, 0.41769, 3.31527), + ('H2', 'H', 0.18953, 0.71385, 0.31124, 4.46988), + ('H3', 'H', 0.43970, 0.62023, 0.34592, 4.34151), + ('C1', 'C', 0.34384, 0.44116, 0.20155, 1.73667), + ('H11', 'H', 0.55246, 0.43345, 0.24304, 3.32279), + ('H12', 'H', 0.32537, 0.38970, 0.08264, 3.05746), + ('C2', 'C', 0.20029, 0.55716, 0.18272, 1.66017), + ('H21', 'H', 0.27650, 0.60004, 0.07688, 2.15403), + ('H22', 'H', -0.00383, 0.54767, 0.15762, 4.71303), +] +# fmt: on + +for _id, _type, _x, _y, _z, _biso in _ATOMS: + structure.atom_sites.create( + id=_id, # FullProf Atom + type_symbol=_type, # FullProf Typ + fract_x=_x, # FullProf X + fract_y=_y, # FullProf Y + fract_z=_z, # FullProf Z + adp_type='Biso', # FullProf Biso + adp_iso=_biso, # FullProf Biso + ) + +project.structures.add(structure) + +# %% +structure.show_as_text() + +# %% [markdown] +# ## Load the FullProf reference + +# %% +FULLPROF_PROJECT_DIR = 'sc-neut-tof_taurine_basic' +FULLPROF_OUT_FILE = 'taurine.out' +FULLPROF_SCALE = 2.711 # FullProf Scale + +f2calc = verify.load_fullprof_sc_f2calc(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE) +FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE) + +# %% [markdown] +# ## Create the experiment + +# %% +experiment = ExperimentFactory.from_scratch( + name='taurine', + sample_form='single crystal', + beam_mode='time-of-flight', + radiation_probe='neutron', + scattering_type='bragg', +) + +experiment.linked_structure.structure_id = 'taurine' +experiment.linked_structure.scale = FULLPROF_SCALE + +verify.set_reference_reflections(experiment, f2calc) + +project.experiments.add(experiment) + +# %% [markdown] +# ## edi-cryspy VS FullProf + +# %% +calc_ed_cryspy = verify.calculate_reflections(project, experiment, 'cryspy') +LABEL_ED_CRYSPY = verify.engine_label('cryspy') +reference, candidate = verify.align_reflections(f2calc, calc_ed_cryspy) + +project.display.reflection_comparison( + 'taurine', + reference=reference, + candidate=candidate, + reference_label=FULLPROF_LABEL, + candidate_label=LABEL_ED_CRYSPY, +) + +# %% [markdown] +# ## Fit edi-cryspy to FullProf + +# %% +experiment.calculator.type = 'cryspy' + +experiment.linked_structure.scale.free = True + +project.analysis.fit() +project.display.fit.results() + +calc_ed_cryspy_refined = verify.calculate_reflections(project, experiment, 'cryspy') +LABEL_ED_CRYSPY_REFINED = verify.engine_label('cryspy', note='scale only') +reference_refined, candidate_refined = verify.align_reflections(f2calc, calc_ed_cryspy_refined) + +project.display.reflection_comparison( + 'taurine', + reference=reference_refined, + candidate=candidate_refined, + reference_label=FULLPROF_LABEL, + candidate_label=LABEL_ED_CRYSPY_REFINED, +) + +verify.report_refinement_closeness( + reference, + candidate, + candidate_refined, +) + +# %% [markdown] +# ## Agreement check + +# %% +verify.assert_patterns_agree([ + (f'{LABEL_ED_CRYSPY_REFINED} vs {FULLPROF_LABEL}', reference_refined, candidate_refined), +]) diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index f21399624..fd8279ce2 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -277,17 +277,19 @@ nav: - Si Jorgensen profile: verification/pd-neut-tof_Si_jorgensen.ipynb - Si Jorgensen-Von Dreele profile: verification/pd-neut-tof_Si_jorgensen-von-dreele.ipynb - Si Jorgensen-Von Dreele + size/strain: verification/pd-neut-tof_Si_jorgensen-von-dreele-size-strain.ipynb + - Diamond DREAM (ESS, McStas): verification/pd-neut-tof_diamond_dream.ipynb - Powder, X-ray, constant wavelength: - LiF single wavelength: verification/pd-xray-cwl_LiF_single.ipynb - LiF polarization: verification/pd-xray-cwl_LiF_single_polarization.ipynb - LiF absorption: verification/pd-xray-cwl_LiF_single_absorption.ipynb - LiF doublet: verification/pd-xray-cwl_LiF_doublet.ipynb - PbSO4 round robin: verification/pd-xray-cwl_PbSO4_round-robin.ipynb - - Single crystal, neutron, constant wavelength: - - Pr2NiO4 basic: verification/sc-neut-cwl_Pr2NiO4_basic.ipynb - - Tb2Ti2O7 basic: verification/sc-neut-cwl_Tb2Ti2O7_basic.ipynb - - Tb2Ti2O7 isotropic extinction: verification/sc-neut-cwl_Tb2Ti2O7_isotropic-extinction.ipynb - - Tb2Ti2O7 anisotropic ADPs: verification/sc-neut-cwl_Tb2Ti2O7_anisotropic-adp.ipynb + - Single crystal: + - Pr2NiO4 basic (CWL): verification/sc-neut-cwl_Pr2NiO4_basic.ipynb + - Tb2Ti2O7 basic (CWL): verification/sc-neut-cwl_Tb2Ti2O7_basic.ipynb + - Tb2Ti2O7 isotropic extinction (CWL): verification/sc-neut-cwl_Tb2Ti2O7_isotropic-extinction.ipynb + - Tb2Ti2O7 anisotropic ADPs (CWL): verification/sc-neut-cwl_Tb2Ti2O7_anisotropic-adp.ipynb + - Taurine basic (TOF): verification/sc-neut-tof_taurine_basic.ipynb - Total scattering: - Ni gaussian-damped sinc: verification/total-neut-cwl_Ni_gaussian-damped-sinc.ipynb - Si gaussian-damped sinc: verification/total-neut-tof_Si_gaussian-damped-sinc.ipynb