Peclet

A suite of codes for simulation of transport phenomena — Eulerian (CFD/Navier–Stokes), Lagrangian (DEM/particle packing) and mixed (Voronoi) methods — sharing one MPI block domain decomposition with efficient asynchronous ghost-layer exchange, SDF-described solids, a common immersed boundary methodology, GPU support, and Python bindings.

The name nods to the Péclet number — the ratio of advective to diffusive transport, the dimensionless heart of transport phenomena.

📖 Documentation site: https://computational-chemical-engineering.github.io/peclet/ — the suite's front door (Python API reference, install/deployment guide, design docs, links to each code's Doxygen API). Built from docs/ via MkDocs (mkdocs.yml).

🧪 Examples gallery: https://computational-chemical-engineering.github.io/peclet-examples/ — runnable, validated notebooks (single-phase and two-phase flow, packings, DEM, CFD-DEM, scaling benchmarks), each with an Open in Colab button.

This is an umbrella repository: each code is a git submodule (its own repo and history); this repo pins compatible commits and holds the shared design docs.

Clone

git clone --recursive git@github.com:computational-chemical-engineering/peclet.git
# or, after a plain clone:
git submodule update --init --recursive

Layout

The compute codes are Kokkos-based; the same source runs on CUDA, HIP (AMD/LUMI), and OpenMP backends, chosen by the bootstrapped install prefix (tools/bootstrap_deps.sh). The reusable parts of the original block_decomposer prototype were extracted into core/.

Shared design docs

docs/ is the cross-code contract every method follows: ARCHITECTURE · CONVENTIONS · STYLE · INTERFACES · ROADMAP · PORTABILITY. See CLAUDE.md for an agent-facing overview.

Install & run (Python)

Everything ships under one peclet namespace — installable parts of one family:

Multicore CPU (OpenMP): the compute packages ship self-contained wheels — pip install peclet (or an individual pip install peclet-flow) just works and runs multi-threaded (OMP_NUM_THREADS).

Quick start — Stokes flow past a sphere in a box of side L, start to finish (about half a minute on two cores); the problem is stated in your own units and N sets the resolution. Run it as is after pip install peclet matplotlib, or open it as a notebook in Colab, whose first cell installs the wheels:

import numpy as np
import peclet.flow as flow

# --- the physical problem, in any consistent unit system -------------------------------------
L, R = 1.0, 0.2              # side of the periodic box and radius of the sphere at its centre
rho, mu = 1.0, 0.1           # fluid density and viscosity
F = 1.0                      # driving pressure gradient along x (force per unit volume)
N = 48                       # cells per side: change this for a grid-refinement study

s = flow.Solver((N, N, N), extent=(L, L, L))                    # a periodic box: a cubic lattice of spheres
s.set_rho(rho); s.set_mu(mu); s.set_dt(1e3)                    # every input physical; a large dt marches
s.set_body_force(F, 0.0, 0.0)                                  #   straight to the steady Stokes flow

x, y, z = s.cell_centres()                                     # the grid the solver laid inside the box
X, Y, Z = np.meshgrid(x, y, z, indexing="ij")
sdf = np.sqrt((X - L/2)**2 + (Y - L/2)**2 + (Z - L/2)**2) - R  # signed distance, < 0 inside the sphere
s.set_solid(sdf, cutcell_pressure=True)                        # no-slip cut-cell immersed boundary

u_prev = 0.0
for it in range(200):
    s.step()
    u_mean = s.get_u().mean()
    if it > 5 and abs(u_mean - u_prev) < 1e-5 * abs(u_mean):   # steady: the mean velocity has settled
        break
    u_prev = u_mean
u, v, w = s.get_u(), s.get_v(), s.get_w()                      # physical velocity, physical pressure
p = s.get_p()
k = mu * u.mean() / F                                          # Darcy permeability of the sphere lattice
print(f"{flow.execution_space}: N = {N}, {it + 1} steps, permeability k = {k:.5e}")

# --- a look at the flow: speed and streamlines on the mid-plane through the sphere ---------------
import matplotlib.pyplot as plt
c = N // 2
speed = np.hypot(u[:, :, c], v[:, :, c])
plt.figure(figsize=(5, 4.2))
plt.imshow(np.ma.masked_where(sdf[:, :, c] < 0, speed).T, origin="lower", cmap="viridis",
           extent=[0, L, 0, L])
plt.streamplot(x, y, u[:, :, c].T, v[:, :, c].T, color="w", density=1.2, linewidth=0.6)
plt.colorbar(label="|u|"); plt.title("Stokes flow past a sphere (periodic box)")
plt.xlabel("x"); plt.ylabel("y"); plt.tight_layout()
plt.show()

Single NVIDIA GPU: pip install peclet-cu13 — CUDA wheels of the same family (only the NVIDIA driver is needed; not alongside peclet in one venv).

AMD/HIP and multi-rank MPI: a wheel cannot carry an MPI ABI, so you build the packages from source against a Kokkos prefix, or use a container. Because the backend (Serial / OpenMP / CUDA / HIP) is compiled in, you build for your hardware — docs/DEPLOYMENT.md is the guide: the backend×MPI matrix, pip install recipes per environment, the Snellius site install (tools/hpc/), and the Apptainer containers (GHCR, built by CI on every release) for Snellius (CUDA) and LUMI (HIP) in containers/.

Continuous integration & docs

Each submodule carries its own .github/workflows/: a CI workflow (build + test — core and morton run full CPU/MPI suites; the Kokkos codes build the OpenMP host backend and run their single-rank suites), a Documentation workflow that builds the Doxygen API docs and publishes them to that repo's GitHub Pages, and a Release workflow that builds the sdist + CPU wheels (+ the CUDA wheel) and publishes them to PyPI on a version tag. The umbrella adds the documentation site (site.yml), the metapackages (release.yml) and the containers (containers.yml). The whole procedure is written down in docs/RELEASE.md.

Contributing & community

Contributions are welcome — see CONTRIBUTING.md for the submodule dev setup, build/test, and PR flow. Participation is governed by the Contributor Covenant. Report security issues privately per the Security Policy. Release history lives in the CHANGELOG.

Citing

If you use Peclet in your research, please cite it. Each release is archived on Zenodo:

• All versions (concept DOI): 10.5281/zenodo.21132445 — always resolves to the latest release; use this unless you need to pin an exact version.
• A specific version: the Zenodo record lists a version DOI per release, and each GitHub release links to its own.

Machine-readable metadata is in CITATION.cff — use GitHub's "Cite this repository" button for ready-made BibTeX/APA.

Note on submodule pins

This umbrella pins each submodule to a compatible commit on main. Update to the latest upstream with git submodule update --remote followed by a commit here that bumps the pointers.