pyiron / pyiron_workflow_atomistics / 25925630010
90%

DEFAULT BRANCH: main
Ran
Jobs 1
Files 38
Run time 1min
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
coverage: 34.031% (-3.7%) from 37.763%
25925630010

push

github

web-flow 
Dynaphopy MD-renormalisation workflow + GRACE example notebook (v0.0.8) (#41)

* docs(design): dynaphopy MD-renormalisation workflow spec

Design for `physics/phonons/md_renormalised.py`: a new macro
`calculate_phonon_md_renormalisation` that runs a Langevin NVT MD
segment via the existing Engine Protocol, projects the trajectory's
velocity ACF onto harmonic phonon modes via dynaphopy, and returns a
`MdPhononOutput` dataclass with renormalised frequencies + linewidths
+ MD health diagnostics (⟨T⟩, σ_T, check_md_health() method, auto-warn
on first bad run).

FC2 source is either-or: pass fc2_supercell_matrix to recompute, or a
phono3py PhononOutput (with keep_handles=True) to reuse — single-rule
coupling table validated up-front at macro entry.

q_points defaults to an ASE auto-derived high-symmetry band path so
non-experts get a meaningful dispersion plot by default; the spec
documents the four scenarios where users should override.

Ships behind a new [phonons-md] superset extra (phonopy + phono3py +
symfc + dynaphopy) so phono3py-only users keep the smaller install.

Adds a per-module header convention (one-line note naming the upstream
package each phonon workflow wraps) — applied to harmonic.py and
anharmonic.py during implementation alongside the new file.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs(plans): dynaphopy MD-renormalisation implementation plan

15 bite-sized TDD tasks (test → impl → commit per task) that build the
new physics/phonons/md_renormalised.py module end-to-end: [phonons-md]
extras + CHANGELOG stub + CI env, require_dynaphopy lazy shim,
MdPhononOutput dataclass + check_md_health(), module-header convention
across the subpackage, _resolve_md_defaults with the four-case
argument-coupling table, _compute_fc2_from_scratch, _run_nvt_trajectory,
_project_with_dynaphopy synthesis node, user-facing macro,
FC2-reuse-path lock-in test, auto-warn lock-in, output tier locks
(power_spectra + keep_handles)... (continued)

878 of 2580 relevant lines covered (34.03%)

0.34 hits per line

Coverage Regressions

Lines Coverage ∆ File
76
0.0
 0.0% physics/phonons/anharmonic.py
33
0.0
 0.0% physics/phonons/output.py
30
0.0
 0.0% physics/phonons/harmonic.py
6
0.0
 0.0% physics/phonons/_compat.py
4
0.0
 0.0% physics/phonons/__init__.py
Jobs
ID Job ID Ran Files Coverage
1 25925630010.1 38
34.03
 GitHub Action Run
Source Files on build 25925630010