pele : Python Energy Landscape Explorer

Tools for global optimization, attractor finding and energy landscape exploration.

Source code: https://github.com/pele-python/pele

https://raw.githubusercontent.com/pele-python/pele/main/lj38_gmin_dgraph.png — Images: The global minimum energy structure of a 38 atom Lennard-Jones cluster. On the right is a disconnectivity graph showing a visualization of the energy landscape. The competing low energy basins are shown in color.

pele started as a python partial-rewriting of GMIN, OPTIM, and PATHSAMPLE: fortran programs written by David Wales of Cambridge University and collaborators (http://www-wales.ch.cam.ac.uk/software.html). The current version also has undergone major development at the Martiniani Lab at New York University (https://martinianilab.org/software/).

Description

pele has tools for energy minimization, global optimization, saddle point (transition state) search, data analysis, visualization and much more. Some of the algorithms implemented are:

Basinhopping global optimization
Potentials (Lennard-Jones, Morse, Hertzian, etc.)
LBFGS minimization (plus other minimizers)
Attractor identification (Mixed Descent, CVODE)
Single ended saddle point search: - Hybrid Eigenvector Following - Dimer method
Double ended saddle point search - Nudged Elastic Band (NEB) - Doubly Nudged Elastic Band (DNEB)
Disconnectivity Graph visualization
Structure alignment algorithms
Thermodynamics (e.g. heat capacity) via the Harmonic Superposition Approximation
Transition rates analysis

Installation

PyPI wheels support Python 3.11–3.14 on Linux x86_64 (glibc 2.28 or newer) and macOS 14 or newer on Intel and Apple Silicon. Windows is not supported:

$ pip install pele

Building from source needs C/C++/Fortran compilers, SUNDIALS, Eigen, LAPACK headers, and OpenMP. A conda environment can supply these dependencies.

$ conda create -n pele -c conda-forge python compilers sundials eigen blas-devel
$ conda activate pele
$ pip install git+https://github.com/pele-python/pele

Python 3.11 or newer is required. CI tests Python 3.11 and 3.14 on Linux and macOS.

If the machine already has gcc, g++ and gfortran (e.g. sudo apt install gcc g++ gfortran), leave out compilers for a much smaller environment. On macOS use homebrew’s gcc (Apple clang has no OpenMP or Fortran):

$ brew install gcc openblas
$ CC=gcc-15 CXX=g++-15 FC=gfortran-15 pip install git+https://github.com/pele-python/pele

Optional: scikit-sparse (sparse Cholesky for rate calculations) and pymol-open-source (viewing structures). The GUI (pele.gui) uses PyQt5 and PyOpenGL. Install them before building so Meson generates the forms:

$ pip install PyQt5 PyOpenGL
$ pip install --no-build-isolation '.[gui]' -Csetup-args=-Dgui=enabled

The OpenGL viewer also needs the system GLU and GLUT libraries (on Ubuntu, sudo apt install libglu1-mesa libglut3.12). Launch an example with python examples/gui/ljsystem.py.

Optional: LAMMPS potentials (pele.potentials.LAMMPSPotential and the pele.systems.AtomicClusterLAMMPS system). Install the LAMMPS Python package before building and the compiled interface is built too; without a build it falls back to a pure Python version:

$ pip install 'lammps[mpi]'
$ pip install --no-build-isolation '.[lammps]' -Csetup-args=-Dlammps=enabled

See examples/gui/lammps_ljsystem.py for a GUI example.

Development

pele is built with meson through meson-python. From a clone, in the same environment:

$ pip install meson-python meson ninja cython numpy
$ pip install --no-build-isolation -e .   # editable

Build options are meson options, passed with -Csetup-args=..., e.g. pip install . -Csetup-args=-Dbuildtype=debug:

-Dbuildtype=debug (default release)
-Dcvode=disabled: no CVODE / attractor identification; some tests will fail
-Dnative=true: opt in to -march=native for local builds. The default is false, for binaries that run on other machines.
-Dgui=enabled / disabled (default auto): generate the PyQt5 GUI forms; needs pyuic5 and pyrcc5
-Dlammps=enabled / disabled (default auto): build the compiled LAMMPS potential; needs the lammps Python package

The editable install keeps its build in build/; pass -Cbuild-dir=... to choose another directory. Editable means code edits will lead to fresh rebuild for C++ code the next time you import pele. python edits will automatically reflect without compilation

SUNDIALS, Eigen and LAPACK are taken from the active conda environment (or, without one, from the system, e.g. sudo apt install libsundials-dev libeigen3-dev liblapack-dev liblapacke-dev). pele links LAPACK itself; it needs the LAPACKE package only for the header lapack.h (conda’s blas-devel provides both). SUNDIALS must be built in double precision.

A CPATH/PYTHONPATH pointing at a pele clone takes precedence over the installed package. If a build fails, remove the build directory before trying again:

$ rm -rf build

Documentation

docs are at https://pele-python.github.io/pele/.

Tests

The project uses GitHub Actions for continuous integration (CI) testing on both Linux and macOS.

The C++ tests use GoogleTest (the cpp_tests/gtest submodule, or a system GoogleTest) and need no Python packages:

$ git submodule update --init --recursive
$ meson setup build-tests -Dpython=disabled -Dtests=true -Dbuildtype=debug
$ meson test -C build-tests

Add -Db_sanitize=address for AddressSanitizer or -Db_coverage=true for coverage. On macOS, prefix meson setup with CC=gcc-15 CXX=g++-15. The benchmarks in cpp_tests/source/benchmarks build on request, e.g. ninja -C build-tests cpp_tests/bench_lj.

To run the Python tests on an installed pele:

$ pip install pytest
$ OMP_NUM_THREADS=1 pytest --pyargs pele

or pytest pele/ from a clone with an editable install. For coverage reporting (as in CI), add --cov=pele --cov-report=term-missing.

Contributing

See CONTRIBUTING.md.

Metadata

Release files for pele 0.1.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pele 0.1.2
File	Size	Uploaded
pele-0.1.2.tar.gz	3.6 MB	Oct 12, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for pele 0.1.2
File	Interpreter	ABI	Platform	Reset
pele-0.1.2-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 23.2 MB Oct 12, 2026	CPython 3.14	CPython 3.14	Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64	Details
pele-0.1.2-cp314-cp314-macosx_14_0_x86_64.whl 20.7 MB Oct 12, 2026	CPython 3.14	CPython 3.14	macOS 14.0+ x86-64	Details
pele-0.1.2-cp314-cp314-macosx_14_0_arm64.whl 14.9 MB Oct 12, 2026	CPython 3.14	CPython 3.14	macOS 14.0+ ARM64	Details
pele-0.1.2-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 23.2 MB Oct 12, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64	Details
pele-0.1.2-cp313-cp313-macosx_14_0_x86_64.whl 20.7 MB Oct 12, 2026	CPython 3.13	CPython 3.13	macOS 14.0+ x86-64	Details
pele-0.1.2-cp313-cp313-macosx_14_0_arm64.whl 14.9 MB Oct 12, 2026	CPython 3.13	CPython 3.13	macOS 14.0+ ARM64	Details
pele-0.1.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 23.2 MB Oct 12, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64	Details
pele-0.1.2-cp312-cp312-macosx_14_0_x86_64.whl 20.7 MB Oct 12, 2026	CPython 3.12	CPython 3.12	macOS 14.0+ x86-64	Details
pele-0.1.2-cp312-cp312-macosx_14_0_arm64.whl 14.9 MB Oct 12, 2026	CPython 3.12	CPython 3.12	macOS 14.0+ ARM64	Details
pele-0.1.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 23.2 MB Oct 12, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64	Details
pele-0.1.2-cp311-cp311-macosx_14_0_x86_64.whl 20.7 MB Oct 12, 2026	CPython 3.11	CPython 3.11	macOS 14.0+ x86-64	Details
pele-0.1.2-cp311-cp311-macosx_14_0_arm64.whl 14.9 MB Oct 12, 2026	CPython 3.11	CPython 3.11	macOS 14.0+ ARM64	Details

Total release size: 238.8 MB

Release files / pele-0.1.2.tar.gz

Download URL	pele-0.1.2.tar.gz
Size	3.6 MB
Tags	Source
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Upload date	Oct 12, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Publishing configuration: github.com/pele-python/pele/blob/b7081b932a060be11342fbe8287ac35da8ada879/.github/workflows/release.yml
Publishing logs: github.com/pele-python/pele/actions/runs/38208244621/attempts/1

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Release files / pele-0.1.2-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

Download URL	pele-0.1.2-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
Size	23.2 MB
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Upload date	Oct 12, 2026
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Subject: pele-0.1.2-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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Release files / pele-0.1.2-cp314-cp314-macosx_14_0_x86_64.whl

Download URL	pele-0.1.2-cp314-cp314-macosx_14_0_x86_64.whl
Size	20.7 MB
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Upload date	Oct 12, 2026
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Release files / pele-0.1.2-cp314-cp314-macosx_14_0_arm64.whl

Download URL	pele-0.1.2-cp314-cp314-macosx_14_0_arm64.whl
Size	14.9 MB
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Upload date	Oct 12, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Publishing configuration: github.com/pele-python/pele/blob/b7081b932a060be11342fbe8287ac35da8ada879/.github/workflows/release.yml
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Release files / pele-0.1.2-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

Download URL	pele-0.1.2-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Subject: pele-0.1.2-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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Release files / pele-0.1.2-cp313-cp313-macosx_14_0_x86_64.whl

Download URL	pele-0.1.2-cp313-cp313-macosx_14_0_x86_64.whl
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Subject: pele-0.1.2-cp313-cp313-macosx_14_0_x86_64.whl
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Release files / pele-0.1.2-cp313-cp313-macosx_14_0_arm64.whl

Download URL	pele-0.1.2-cp313-cp313-macosx_14_0_arm64.whl
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Release files / pele-0.1.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

Download URL	pele-0.1.2-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
Size	23.2 MB
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Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Release files / pele-0.1.2-cp312-cp312-macosx_14_0_x86_64.whl

Download URL	pele-0.1.2-cp312-cp312-macosx_14_0_x86_64.whl
Size	20.7 MB
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Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Download URL	pele-0.1.2-cp312-cp312-macosx_14_0_arm64.whl
Size	14.9 MB
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Release files / pele-0.1.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

Download URL	pele-0.1.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
Size	23.2 MB
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Upload date	Oct 12, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Subject: pele-0.1.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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Release files / pele-0.1.2-cp311-cp311-macosx_14_0_x86_64.whl

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Size	20.7 MB
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Upload date	Oct 12, 2026
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Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Subject: pele-0.1.2-cp311-cp311-macosx_14_0_x86_64.whl
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Release files / pele-0.1.2-cp311-cp311-macosx_14_0_arm64.whl

Download URL	pele-0.1.2-cp311-cp311-macosx_14_0_arm64.whl
Size	14.9 MB
Tags	CPython 3.11 macOS 14.0+ ARM64
SHA-256 checksum How to use checksums	`b1d85a61c11773cf017539a759e2fcecb3116618bcb86c8f3194b818814187d9`
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Upload date	Oct 12, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

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Publishing platform: GitHub Actions
Publishing repository: github.com/pele-python/pele
Publishing commit: github.com/pele-python/pele/tree/b7081b932a060be11342fbe8287ac35da8ada879

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Publishing logs: github.com/pele-python/pele/actions/runs/38208244621/attempts/1

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Subject: pele-0.1.2-cp311-cp311-macosx_14_0_arm64.whl
SHA-256 checksum: b1d85a61c11773cf017539a759e2fcecb3116618bcb86c8f3194b818814187d9 Verifying attestations

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This release

0.1.2 This release

Oct 12, 2026 13 release files

0.1.1

Oct 8, 2026 12 release files

pele 0.1.2

pele : Python Energy Landscape Explorer

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