irma 1.0.0__tar.gz

irma-1.0.0/CHANGELOG.md

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+# Changelog
+
+Notable changes to IRMA. Format follows [Keep a Changelog](https://keepachangelog.com/);
+versions follow [Semantic Versioning](https://semver.org/).
+
+## [1.0.0] — 2026-08-03
+
+Initial public release. IRMA turns one phonon model into three
+outputs on one engine:
+
+- **ENDF-6 File 7 evaluations** from LEAPR-style decks: the classic
+  kernels (validated bit-for-bit against NJOY2016 reference tapes),
+  generalized coherent elastic for arbitrary crystals (`iel=10`,
+  SEF/MEF output conventions, Bragg-edge grouping, opt-in
+  crystalline extinction), and the phonopy-backed noncubic inelastic
+  modes with the exact coherent one-phonon term, anisotropic
+  Debye-Waller tensors, a per-species partition for polyatomic
+  materials, and automatic alpha/beta grids.
+- **Instrument-resolved neutron spectra** (`irma spectra`):
+  indirect- and direct-geometry spectrometers, chopper resolution,
+  2-D S(Q,E) maps, and a DOS-driven mode 0.
+- **NCrystal transport exports** (`irma ncrystal`) sampled by the
+  companion `ncrystal_plugin_IRMA`, plus the standalone
+  `ncrystal_plugin_ENDFTSL` plugin for sampling ENDF TSL files
+  directly in NCrystal.
+
+The **MLIP phonon front end** (`irma mlip`) builds the phonon model
+itself from a bare crystal structure with one of nine pretrained
+machine-learned interatomic potentials, and emits ready-to-edit
+inputs for all three outputs (`--inelastic-mode 0|1|2`, mixed
+elastic format by default).
+
+A GUI (`python -m irma --gui`) drives every path. `examples/` maps
+sixteen runnable examples to their calculation types; `skills/irma/`
+ships an opt-in assistant skill for AI coding agents; the validation
+record under `docs/validation/` documents the evidence behind the
+physics (NJOY reference tapes, Euphonic and OCLIMAX cross-code
+comparisons, and measured VISION, ARCS, and VENUS data).
+
+The development history preceding this release is internal to ORNL.

irma-1.0.0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use IRMA in your research, please cite it as below."
+title: "IRMA — (In)elastic Representation of Materials As S(alpha,beta) evaluations"
+abstract: >-
+  IRMA generates thermal neutron scattering law S(alpha, beta) libraries in
+  ENDF-6 format using the phonon expansion method, with generalized coherent
+  elastic for arbitrary crystals and phonopy-backed noncubic inelastic paths
+  carrying an exact coherent one-phonon term. The same phonon model also drives
+  a neutron-scattering forward model (powder S(Q,E) to instrument-resolved
+  spectra) and an exporter that writes scattering kernels for a companion
+  NCrystal plugin, for Monte Carlo transport. A front end builds the phonon
+  model from a crystal structure using pretrained machine-learned interatomic
+  potentials.
+type: software
+authors:
+  - family-names: Ramic
+    given-names: Kemal
+    email: ramick@ornl.gov
+    affiliation: "Oak Ridge National Laboratory"
+    orcid: "https://orcid.org/0000-0002-3495-9821"
+version: "1.0.0"
+date-released: "2026-08-03"
+license:
+  - BSD-3-Clause
+  - Apache-2.0
+repository-code: "https://github.com/ramic-k/IRMA"
+keywords:
+  - thermal neutron scattering
+  - "S(alpha,beta)"
+  - thermal scattering law
+  - ENDF
+  - LEAPR
+  - phonon
+  - inelastic neutron scattering
+doi: "10.11578/dc.20260803.1"

irma-1.0.0/CONTRIBUTING.md

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+# Contributing to IRMA
+
+## Development setup
+
+```bash
+pip install -e ".[phonopy,spectra,mlip]"   # matches what CI tests; phonopy only
+                                           # needed for inelastic_mode=1/2, spectra
+                                           # for the irma.spectra forward model,
+                                           # mlip for the irma.mlip front end
+pip install -r requirements-dev.txt
+```
+
+## Tests
+
+```bash
+python -m pytest                   # fast suite (~25 s, no phonopy/NJOY)
+```
+
+CI (`.github/workflows/ci.yml`) runs the fast suite on every push and
+pull request, across Linux/macOS/Windows and Python 3.11-3.13, plus the
+two NCrystal plugin gates.
+Keep it green; keep it fast — anything needing phonopy, NJOY, or more than a
+few seconds belongs in the manual validation harnesses, not the fast suite.
+
+The `irma.mlip` tests (`tests/mlip/`) follow the same rule with one twist:
+they exercise the calculator factory through stubs and the displacement/dispatch
+machinery through ASE's built-in EMT, so they need `ase`/`phonopy`/`PyYAML`
+(the `[mlip]` extra) but no potential package and no network; without the
+extra they skip cleanly. Tests that instantiate real potentials sit behind
+the `mlip_real` marker and only run when you opt in with
+`IRMA_MLIP_REAL_TESTS=1`.
+
+## Validation harnesses (manual, not CI)
+
+- `tests/native_LEAPR_NJOY_ENDF_validation/` — IRMA must reproduce the
+  committed native LEAPR/NJOY reference tapes (7e-5 or better inelastic, exact
+  elastic structure). Run after touching the classic path, the writer, or
+  anything in the ENDF output chain.
+- `tests/mode2_euphonic_n1_validation/` — the mode-2 exact one-phonon
+  S(α,β) vs the committed Euphonic reference. Run after touching the noncubic
+  engine. Regenerating the frozen reference requires `euphonic` and is only
+  needed if the vendored phonon models change.
+
+## Refactoring policy
+
+Behavior-preserving changes to the physics chain are verified by
+byte-identical output: build a baseline of representative decks covering
+every affected code path (see the validation README for deck patterns —
+classic, negative-temperature reuse, secondary scatterer, single-channel (SEF) / mixed (MEF) / grouped elastic, modes 1/2 with multiphonon and SCT), produce tapes before and
+after, and `cmp` them. Single-process runs (`ncpu=1`) are deterministic and
+byte-stable; use them for baselines.
+
+For the noncubic modes 1/2 specifically, `tools/tape_gauge.py` is the
+standing instrument: a fast 8³ iteration profile and a `--big` production
+profile (graphite, 40³ mesh, standard sampling, the full automatic grids).
+Run the baseline from a pristine worktree of the last blessed commit, the
+candidate from the working tree, and `--diff` the two — it passes on
+byte-identical tapes, or on parsed MF7/MT4 agreement within 1e-6 relative
+(the ENDF write precision). Deliberate physics changes additionally need
+their own quantification and a CHANGELOG record stating what moved and by
+how much.
+
+## Conventions
+
+- Three hard dependencies only (numpy, endf-parserpy, threadpoolctl).
+  phonopy stays an optional extra; do not add imports of it outside lazy,
+  mode-1/2-only paths. Anything heavier belongs in validation tooling, not
+  the package.
+- Native BLAS/OpenMP threads are pinned to 1 by design (measured: threaded
+  BLAS inside the `ncpu` worker pool oversubscribes and is >10x slower).
+  Parallelism belongs to the Card 6f `ncpu` process pool, which uses the
+  spawn start method (Windows-compatible; a driver script calling IRMA at
+  module level therefore needs the standard `if __name__ == "__main__":`
+  guard). `IRMA_WORKER_THREADS` overrides the per-worker thread pin for
+  tuning experiments only — the default of 1 is the measured optimum.
+- Input-format changes must keep the LEAPR-derived card structure and be
+  validated with friendly `DeckError` messages (card name, expected/found,
+  input line) — see `tests/test_deck_errors.py`.
+- Comments document the code as it is — no exploratory narration, no
+  conversational asides. If a value or layout matches NJOY, cite the NJOY
+  routine it matches.

irma-1.0.0/INSTALL.md

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+# Installing IRMA
+
+The full installation guide — including the optional pieces and what each
+workflow needs — lives in the manual at
+[`docs/installation.md`](docs/installation.md). This file is the short
+version.
+
+## Prerequisites
+
+- **Python 3.11 or later** — [Download Python](https://www.python.org/downloads/)
+- **tkinter** — Required for the GUI. It is included with most Python
+  installations. If you get an `ImportError: No module named tkinter`, see
+  the [Tkinter installation notes](#tkinter) below.
+
+## Install
+
+From the IRMA source directory, pick the form that covers your workflows:
+
+```bash
+pip install -e .              # core (classic LEAPR paths, iel=0-6 and iel=10 mode 0)
+pip install -e ".[phonopy]"   # + the noncubic inelastic paths (inelastic_mode=1/2)
+pip install -e ".[spectra]"   # + the neutron-scattering forward model (irma spectra)
+pip install -e ".[mlip]"      # + the MLIP phonon front end (irma mlip)
+```
+
+The extras combine: `pip install -e ".[phonopy,spectra,mlip]"` covers
+everything.
+For a regular (non-editable) install, drop the `-e`. The required
+dependencies (**numpy**, **endf-parserpy**, and **threadpoolctl**, at the
+versions validated in `pyproject.toml`) are resolved automatically — there is
+no separate dependency-install step.
+
+What each extra unlocks:
+
+| Extra | Adds | Needed for |
+|-------|------|------------|
+| `[phonopy]` | `phonopy` | `iel=10` with `inelastic_mode=1` or `2` (the phonopy-backed noncubic MT4 paths), and `irma.spectra` inelastic modes 1/2 or `dos_source: phonopy` |
+| `[spectra]` | `scipy`, `PyYAML` | the `irma.spectra` forward model (`irma spectra` CLI and the GUI's **Neutron Scattering Experiments** tab) |
+| `[mlip]` | `ase`, `phonopy`, `PyYAML` | the `irma.mlip` phonon front end (`irma mlip` CLI and the GUI's **MLIP phonon models** tab). The potential packages themselves are not included: their pins conflict with each other, so `irma mlip env create` installs each one into its own dedicated environment |
+
+### Dependency documentation
+
+If you need help installing or configuring the dependencies:
+
+| Package | Documentation |
+|---------|---------------|
+| numpy | [numpy.org/install](https://numpy.org/install/) |
+| endf-parserpy | [github.com/IAEA-NDS/endf-parserpy](https://github.com/IAEA-NDS/endf-parserpy) |
+| phonopy | [phonopy.github.io/phonopy/install.html](https://phonopy.github.io/phonopy/install.html) |
+
+For the noncubic modes (`iel=10` with `inelastic_mode=1/2`), the deck also
+needs the phonopy control cards (`Card 6f` and `Card 6g`):
+
+- use `nspec=0` and omit Card `6e`
+- keep the full crystal in Card `6d`, even for mixed materials
+- keep one principal scatterer per deck; Card `5` chooses which atom gets the
+  exported MT4 law
+- if you need separate mixed-material tapes for different principals
+  (for example Be and O in BeO), run IRMA once per principal
+
+## Verify the installation
+
+```bash
+python -m irma --version
+```
+
+This should print the IRMA version number.
+
+## Launching the GUI
+
+There are two ways to launch the graphical interface:
+
+```bash
+# Option 1: Module flag
+python -m irma --gui
+
+# Option 2: Installed entry point
+irma-gui
+```
+
+Both open the same GUI window. The GUI uses **tkinter**, which is part of
+the Python standard library — no extra GUI framework is needed.
+
+## Running from the command line
+
+```bash
+python -m irma input_file output_file
+```
+
+Or using the installed entry point:
+
+```bash
+irma input_file output_file
+```
+
+With the `[spectra]` extra installed, the neutron-scattering forward model
+is available as a subcommand:
+
+```bash
+irma spectra --help
+```
+
+With the `[mlip]` extra installed, the phonon front end is available the
+same way:
+
+```bash
+irma mlip --help
+```
+
+## Platform support
+
+| Capability | Linux | macOS | Windows |
+| --- | --- | --- | --- |
+| ENDF/TSL evaluation (classic paths, `iel` 0-6/10 with `inelastic_mode=0`) | yes | yes | yes |
+| Noncubic `inelastic_mode=1/2`, spectra forward model, NCrystal export | yes | yes | untested* |
+| GUI | yes | yes | untested** |
+| C++ NCrystal plugins (build) | yes (CI-gated) | yes | untested |
+
+The noncubic worker pool uses the spawn start method with the compute
+context in shared memory, so `ncpu > 1` (Card 6f) and `jobs > 1` are
+implemented identically on all three platforms — but only Linux (CI) and
+macOS (routine development) are TESTED. \*Windows support is untested
+until a smoke test runs on real Windows hardware; treat `jobs > 1` /
+`ncpu > 1` there as experimental. \**Additionally, cancelling a parallel
+GUI run on Windows currently terminates only the immediate child process:
+spawned workers can keep running until they finish their current work item
+(no tree-aware kill is implemented yet). On Windows, prefer `jobs=1` for
+GUI runs or be prepared to end stray worker processes manually.
+One standard spawn requirement applies: a
+script that drives IRMA programmatically must wrap its entry point in
+`if __name__ == "__main__":` — the `irma` CLI and `python -m irma...`
+entry points already do.
+
+## Tkinter
+
+The GUI requires tkinter, which ships with most Python distributions. If
+it is missing on your system:
+
+- **macOS** — Install the official Python from
+  [python.org](https://www.python.org/downloads/). The Homebrew Python
+  (`brew install python`) may not include tkinter; if so, run
+  `brew install python-tk`.
+- **Ubuntu/Debian** — `sudo apt install python3-tk`
+- **Fedora** — `sudo dnf install python3-tkinter`
+- **Arch Linux** — `sudo pacman -S tk`
+- **Windows** — Tkinter is included by default with the standard Python
+  installer from python.org. Make sure the "tcl/tk and IDLE" option is
+  checked during installation.
+- **Conda** — `conda install -c conda-forge tk`
+
+## Troubleshooting
+
+**`ModuleNotFoundError: No module named 'irma'`**
+Make sure you ran `pip install -e .` from the IRMA directory, and that
+you are using the same Python environment.
+
+**`ModuleNotFoundError: No module named 'tkinter'`**
+See the [Tkinter](#tkinter) section above.
+
+**GUI does not appear on macOS**
+If you are using a virtual environment, make sure it was created with
+access to the system tkinter. Try: `python -m venv --system-site-packages myenv`

irma-1.0.0/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2026, Oak Ridge National Laboratory
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
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+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

irma-1.0.0/LICENSES/Apache-2.0.txt

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irma-1.0.0/MANIFEST.in

@@ -0,0 +1,28 @@
+# Deliberate sdist contents. Without this file, setuptools' legacy defaults
+# shipped a broken half test-tree (tests/test_*.py without conftest.py or the
+# ~33 MB of reference data they need) and omitted the project meta-docs.
+# The sdist is library-only: the test suite and its reference tapes live in
+# the repository. LICENSE and THIRD_PARTY_NOTICES.md are included via
+# `license-files` in pyproject.toml.
+prune tests
+include LICENSES/Apache-2.0.txt
+include CHANGELOG.md
+include CITATION.cff
+include INSTALL.md
+include CONTRIBUTING.md
+graft examples
+# The shipped graphite examples (examples/tsl/graphite_mode2.input and the
+# examples/spectra/*.yaml phonopy-backed configs) reference this vendored phonopy
+# model + its companion force constants. Re-include just those two files after the
+# `prune tests` above (MANIFEST is order-sensitive: a later `include` re-adds them)
+# so the examples run from an unpacked sdist, not only from a repo checkout.
+include tests/mode2_euphonic_n1_validation/graphite/phonopy.yaml
+include tests/mode2_euphonic_n1_validation/graphite/FORCE_CONSTANTS
+# The shipped READMEs (README.md "Worked examples" and examples/tsl/README.md)
+# give runnable `python -m irma <deck> <out>` commands that point at these
+# classic reference decks, so ship the decks themselves (~380 KB total). The
+# multi-MB companions (NJOY .leapr job streams, reference .endf tapes) stay
+# repository-only; the READMEs say so. leapr_to_irma_input.py is the converter
+# both READMEs reference for turning an NJOY LEAPR deck into an IRMA deck.
+include tests/native_LEAPR_NJOY_ENDF_validation/leapr_decks/*.input
+include tests/native_LEAPR_NJOY_ENDF_validation/leapr_to_irma_input.py