pnmr-chi-gen 0.1.0

A standalone generator of susceptibility tensor series for pNMR simulations

pnmr-chi-gen

pnmr-chi-gen is a standalone generator of magnetic susceptibility tensor series for paramagnetic NMR simulation workflows and machine-learning datasets.

The package is built to generate physically valid, temperature-dependent susceptibility tensors in a format that can be consumed by paranmr/simpnmr. Its immediate value is upstream of simulation: it gives ML workflows a controlled way to sample tensor trajectories with explicit latent parameters, temperature grids, and reproducible seeds.

Why this library matters for ML

In paramagnetic NMR, the magnetic susceptibility tensor is a compact physical object that strongly controls PCS-driven spectral behaviour. For ML applications, that makes it a useful representation layer:

• physically meaningful
• lower-dimensional than spectra
• easy to constrain
• easy to sample reproducibly
• directly consumable by downstream simulation tools

Instead of starting from broad synthetic artifacts and inferring structure afterward, pnmr-chi-gen starts from the tensor itself. That makes dataset generation more controlled, more interpretable, and easier to audit.

Typical use cases:

• synthetic data generation for inverse pNMR problems
• supervised learning on latent-to-tensor mappings
• augmentation across temperature series
• benchmarking tensor reconstruction models
• generating paranmr/simpnmr-compatible inputs at scale

Current scope

Version v0.0.1 is intentionally focused.

Implemented:

• iso / ax / rho_over_ax tensor parameterization
• one shared orientation per generated series
• integer temperature grids
• Curie-like temperature dependence across the series
• deterministic YAML-driven generation
• paranmr/simpnmr-compatible CSV export
• CLI entrypoint for reproducible batch generation

Not implemented yet:

• alternative tensor parameterizations
• richer temperature-dependence models
• dataset manifests and metadata bundles
• dedicated ML dataset export layers

Installation

python3 -m pip install -e .

For development:

python3 -m pip install -e .[dev]

Quick start

Example config:

output_name: run_minimal_output

generator:
  n_series: 1
  seed: 7

temperature:
  start: 280
  stop: 282
  step: 1

chi_iso: 10.0
chi_ax: 3.0
rho_over_ax: 0.1666666667

orientation:
  alpha_deg: 0.0
  beta_deg: 0.0
  gamma_deg: 0.0

Run:

pnmr_chi_gen run examples/run_minimal.yaml

This creates:

examples/run_minimal_output/
  susceptibility_tensor_1_280K_to_282K.csv

YAML contract

The input model is intentionally small.

Scalar values mean fixed parameters:

chi_ax: 3.0

Two-element lists mean uniform sampling bounds:

chi_ax: [0.0, 3.0]

The same pattern applies to Euler angles:

orientation:
  alpha_deg: [0.0, 360.0]
  beta_deg: [0.0, 180.0]
  gamma_deg: [0.0, 360.0]

output_name controls the name of the folder created next to the YAML file.

If output_name is omitted, the folder name defaults to the YAML filename stem.

Output contract

Each generated CSV stores one full temperature series of susceptibility tensors.

The exported layout is compatible with paranmr/simpnmr and includes:

• temperature
• chi_iso
• chi_ax
• chi_rho
• full Cartesian tensor components
• traceless anisotropic components
• principal values
• Euler angles

That makes the generator useful both as a standalone library and as an upstream source for pNMR simulation pipelines.

Physical and engineering constraints

The library validates a small set of explicit invariants:

• 0 <= rho_over_ax <= 1/3
• Euler angles in valid ZYZ ranges
• symmetric 3x3 susceptibility tensors
• positive temperatures
• strictly increasing temperature series without duplicates
• sampling bounds with lower <= upper

These checks live in the core constraint layer rather than being scattered across CLI or config parsing code.

Architecture

The package is structured as a layered system:

src/pnmr_chi_gen/
  app/    # orchestration
  cfg/    # YAML-facing config loading
  cli/    # command-line entrypoint and logging
  core/   # constraints, domain, generators, parameterizations, rotations
  io/     # export adapters

Responsibilities are separated on purpose:

• cli handles user interaction
• cfg translates YAML into typed internal specs
• core owns scientific and numerical logic
• io owns file-format boundaries
• app wires the pipeline end to end

This keeps the codebase usable both as a CLI tool and as a library component inside larger ML and simulation workflows.

Reproducibility

Generation is seed-controlled:

generator:
  n_series: 100
  seed: 42

That matters for ML dataset work, where exact regeneration of sampled tensors is often required for experiments, benchmarks, and audits.

Relationship to paranmr/simpnmr

pnmr-chi-gen is not meant to replace paranmr/simpnmr. It sits upstream of that ecosystem.

• pnmr-chi-gen generates susceptibility tensor series
• paranmr/simpnmr consumes susceptibility tensors in fitting and simulation workflows

That separation is useful. One tool is responsible for controlled data generation; the other is responsible for domain simulation and analysis.

Development

Run tests:

PYTHONPATH=src python3 -m pytest -q

Run the example:

pnmr_chi_gen run examples/run_minimal.yaml

Roadmap

Planned next directions:

• broader prior families for tensor latents
• additional tensor parameterizations
• richer temperature-dependence models
• dataset provenance and metadata export
• tighter support for larger synthetic ML corpora

License

MIT