PyHermes

PyHermes is the high-performance Python implementation of Hermes (HypER-speed MultirEsolution cosmic Statistics), an in situ framework that turns particle catalogues into reusable multiresolution fields for cosmic statistics and physical-field analysis.

A catalogue is projected once into a scaling-function-coefficient field (SFCField). Smoothing, geometric binning, multipole decomposition, differentiation, and inverse-Laplacian operations are then expressed through WindowFunc objects. The same field can therefore feed Counting, isotropic and anisotropic 2PCFs, standard and multipole 3PCFs, marked statistics, and derived physical fields without returning to particle-level tuple counting for every configuration.

• Documentation: pyhermes.astroslacker.com
• Source: SYSUSPA-Projects/PyHermes
• Paper: arXiv:2607.23494
• Tutorials: examples/notebooks/
• Runnable configurations: examples/configs/ and examples/scripts/

What It Covers

• catalogue-to-field projection with configurable compactly supported scaling functions and resolution J;
• built-in and user-defined smoothing, binning, multipole, and operator windows;
• one-point counting and field sampling;
• isotropic and anisotropic 2PCF measurements;
• Monte Carlo and spherical-harmonic 3PCF estimators;
• MPI/thread parallelism and CPU or CUDA contraction for 3PCF multipoles;
• weighted fields, velocity derivatives, Poisson potential, acceleration, and density-dependent marks.

Optional spectral 2PCF computation

Version 1.2.0 was released on 2026-10-20. The changes below, including the 2PCF and 3PCF updates, are collected as changes since 1.1.0 in CHANGELOG.md. See the release and migration guide for compatibility.

Version 1.2.0 includes an opt-in spectral path with automatic window strategies. Add these settings to an existing Corr_2PCF task, keeping its window definition, bin edges, and sampling:

fast_options = dict(
    memory_strategy="speed",
    pair_reduction="spectral",
    reuse_input_fields=True,
    spectral_window="auto",
    spectral_fft="shared",
)

Parseval's identity evaluates the required field products directly in Fourier space, avoiding inverse FFTs and full convolution-result arrays. Prepared inputs, source spectra, and adjacent finite-shell boundaries are reused within one run. auto groups exact radial frequency classes for shell, gaussian_shell, thick_shell, and other built-in isotropic windows. For a grid-axis line of sight, ring, gaussian_ring, disk, cylshell, and cylinder share a separable factor-table backend; cubic reuses this backend through its three sinc factors. Tilted or unsupported windows retain the applicable generic path. Every original alias scaling weight and folding multiplicity is retained; there is no interpolation or change to the window definition.

The default remains the convolution path. Caches do not reuse production results between runs; custom or unsupported windows retain their existing fallbacks. See the 2PCF spectral guide for parameters, equations, memory limits, and total-time versus main-loop timing, and the controlled window-strategy report for numerical checks and workload-specific performance, including the matched 46×51 axial-window measurements and amortized task time per sample.

Direct field-pair evaluation

A real SFCField can prepare a reusable local pair for an existing list of compatible WindowFunc objects:

with delta.pair_with(delta, threads=8) as pair:
    xi = pair.evaluate(windows) / RR

pair.evaluate(windows) returns the coefficient-array pair mean in input order and shares automatic window plans. Apply your estimator's normalization explicitly; RR = rho**2 is the uniform-reference case. For one window, use pair.evaluate([window])[0]. Different real fields can be passed to first.pair_with(second). Complex-response windows retain the phase-preserving convolution fallback. Keep inputs unchanged until the pair is closed; the with block releases its retained powers. Distributed sampling and task-level normalization remain available through Corr_2PCF and its existing options.

The direct-reconstruction section in the 2PCF tutorial explains the convolution and Parseval formulations and their task options. See the local pair evaluation guide for a complete example, normalization, lifetime and timing boundaries.

Standard angular three-point statistics

Corr_3PCF prepares box-random contrast fields once per product and shares the exact 2PCF backend for its lower-order pair series and Q postprocessing. This adds no user setting and retains the sampled centres, rotations, seeds, weights, interpolation and alias folding. Root-only pair planning uses local communication. See the angular 3PCF guide and verified measurements. The report separates local synthetic profiles from verified J8 catalogue DDD/Q timings on 128 CPU cores; the catalogue timings are not a controlled full-size baseline speedup.

Three-point multipoles in 1.2.0

Corr_3PCF_Multipole offers two summation methods through the same task and result interface:

Defaults remain gamma and gpu; explicitly select cpu without CUDA. All paths construct harmonic arms using CPU FFTs. Particle summation reads those arms at catalogue positions, requires retrievable particle data, and supports an unfiltered first vertex only. Use window2/window3 for endpoint smoothing and omit window/window1. Particle and Gamma summation have different finite-resolution discretizations.

Run particle summation directly in the 3PCF tutorial. It uses the saved example field and its particle companion. For command-line execution, use param_3pcf_multipole_particle.yaml with the normal multipole driver. The multipole guide explains serial/MPI execution, weights, windows, and saved results.

The 1.2.0 update fixes Gamma triple overlaps and reuses CPU workspaces and source FFTs. Recompute affected Gamma multipole measurements made with 1.1.0; existing catalogue projections can be reused. Source FFT reuse trades memory for computation; speedups depend on workload and CPU placement. See CHANGELOG.md for the correction and migration notes. The verified example refresh records the new 2PCF and corrected CPU multipole outputs, observed timings, input provenance and executed notebook plots. Historical results are retained.

Installation

Install PyHermes from PyPI:

python -m pip install pyhermes-cosmo

This installs PyHermes and its regular Python dependencies automatically. MPI and CUDA are optional, so neither is required for the default installation.

For the notebooks and plotting examples, install the plotting extra:

python -m pip install "pyhermes-cosmo[plot]"

Keep the code and example configurations on the same version or commit. See the installation guide for development, MPI and CUDA setup.

The Python import name remains unchanged:

import pyhermes

For a ready-to-use MPICH environment on Linux or macOS:

conda create -n pyhermes -c conda-forge python=3.12 mpi4py mpich pip
conda activate pyhermes
python -m pip install pyhermes-cosmo
mpiexec -n 2 python -c "from mpi4py import MPI; print(MPI.COMM_WORLD.rank)"

Here conda provides a mutually compatible MPI runtime and Python binding, while pip installs PyHermes and the remaining Python dependencies. PyHermes does not yet require a separate conda package for this workflow.

Without mpi4py, PyHermes automatically uses its single-process MPI fallback. Users of an existing cluster MPI should follow the installation guide for the matching mpi4py and GPU setup.

Smallest Workflow

The tracked Quick Start configurations use paths relative to examples/:

cd examples
python scripts/run_sfc_projection.py configs/param_sfc_projection.yaml
python scripts/run_2pcf.py configs/param_2pcf.yaml

The first command downloads and caches the original single-file Quijote group_tab catalogue from the URL in the YAML, verifies its SHA256 digest, and writes the base SFCField. The second command consumes that exact field and writes an isotropic Corr2PCFData result. The matching quick_start.ipynb executes the same configs and plotting code rather than maintaining a parallel example.

The dedicated particle_io.ipynb reuses that catalogue and shows how the native FoF reader, an NPZ conversion, and a raw BIN layout all feed the same projection API. The converted NPZ and BIN files are local teaching products, not additional public downloads. sfc_projection.ipynb then builds the J=9, weighted, redshift-space, and explicit sampled-random fields used by later examples; scripts/prepare_sfc_fields.py provides the equivalent non-interactive batch entry point. The optional dark-matter snapshot builder accepts the local Gadget HDF5 snapshot prefix explicitly; no cluster-specific path is embedded in the code:

python scripts/build_quijote_dm_sfc_field.py /path/to/snapdir_004/snap_004

from pyhermes.base.sfc_projection import SFCProjection
from pyhermes.io import WindowFunc
from pyhermes.param.parambase import read_param

params = read_param("./configs/param_sfc_projection.yaml")
field = SFCProjection(params).run()

gaussian = WindowFunc(
    {"type": "gaussian", "len_args": {"R": 10.0}},
    field.sfc_info,
    threads=8,
)
smoothed_field = field @ gaussian

This is the core language of PyHermes: field @ window. Statistical tasks build the required window families and normalizations around the same objects.

Start With The Notebooks

The recommended route through examples/notebooks/ is:

1. quick_start.ipynb
2. particle_io.ipynb
3. sfc_projection.ipynb
4. window.ipynb
5. physical_fields.ipynb
6. counting.ipynb
7. corr2pcf.ipynb
8. corr3pcf.ipynb

The first four notebooks establish the common catalogue-to-field-to-window workflow. Continue with physical fields, one-point Counting, or the 2PCF-to-3PCF statistics path according to the calculation you need.

Generated catalogues and estimator products are intentionally not committed. The notebooks state which lightweight cells run locally and which script/YAML pairs are intended for a workstation or cluster.

Documentation

The full guide at pyhermes.astroslacker.com follows the terminology and estimator definitions of the Hermes paper. It covers the mathematical construction, current APIs, window catalogue, parameter mappings, numerical validation, and performance interpretation.

To build the documentation locally:

python -m pip install ".[docs]"
sphinx-build -W -b html docs docs/_build/html

Citing PyHermes

If PyHermes contributes to your work, please cite the software version and the four papers that describe its scientific foundation and implementation:

1. Hermes/PyHermes: Long-long Feng, Tengpeng Xu, Tian-Cheng Luan et al. (2026), Hermes - Towards an Optimal High-Performance Algorithm for Cosmic Statistics of Large Data Sets, arXiv:2607.23494 [astro-ph.CO].
2. MRACS foundation: Feng (2007), The Beylkin-Cramer Summation Rule and a New Fast Algorithm of Cosmic Statistics for Large Data Sets.
3. In-situ correlation functions: Yue et al. (2024), Pair counting without binning -- a new approach to correlation functions in clustering statistics.
4. Isotropic 3PCF multipoles: Ju et al. (2026), An optimal in situ multipole algorithm for the isotropic three-point correlation function.

Machine-readable metadata is provided in CITATION.cff; complete BibTeX entries are available in the citation guide.