About
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About

readcon-core is the reference implementation of versioned .con / .convel. This stack puts CON everywhere: every optimizer, potential driver, analysis tool, campaign store, and ML hand-off that needs a durable atomic configuration with constraints, forces, and identity.

CON is human-readable and complete on one frame: cell, type-grouped coordinates, per-direction fixed masks, column-5 atom_id, optional per-atom sections (velocities, forces, energies, charges, spins, magmoms), and JSON metadata (spec v2–v3, docs/orgmode/spec.org). That payload is why saddle, dimer, and NEB codes already work on CON; the library exists so the rest of the atomistic stack adopts the same file.

Layer	Role in spreading CON
Spec + hot path	Spec v3 parse/write, `validate`, units, `sections`, SoA, Cachegrind CI
Hourglass ABI	C / C++ / Python / Julia / Fortran (`rkr_*`): link CON into any language
Device / ML hand-off	DLPack (optional CUDA); optional metatensor `TensorBlock` without leaving CON authority
Ingress	Chemfiles import/selection: foreign structures into CON
Campaigns	`index_proj` + readcon-db (`cargo add` / `pip install`; docs · docs.rs)

Already on that path: rare-event clients, rgpot, rgpycrumbs, ASE adapters, amsel, campaign stores, and anything that takes DLPack or metatensor blocks.

Rust rewrite of readCon. Chemfiles owns format diversity at the edge; this crate owns CON fidelity on the wire and in memory.

Measurements: Cachegrind I-refs (examples/cachegrind_harness.rs); Python ASV + spyglass on PRs (benchmarks/); CON peers via benches/compare_readers.py (and other scripts under benches/). See docs/orgmode/benchmarks.org.

Features

CON and convel: Coordinates; optional sections declared in sections (velocities, forces, energies, charges, spins, magmoms). Velocities also auto-detect on legacy .convel without a sections key.
Lazy iteration: ConFrameIterator; next_with_raw_span keeps the on-disk blob for corpus ingest.
Hot path: fast-float2, memmap2, Cachegrind-tracked scenarios.
Parallel frames: Rayon behind the parallel Cargo feature.
Bindings: Python (PyO3), Julia (ccall), C (shipped header), C++ (RAII header), Fortran (fpm); hourglass ABI patterned on metatensor.
Metadata helpers: Typed energy, frame_index, time, timestep, neb_bead, neb_band across bindings; raw JSON still available.
Validation: validate=true enforces finiteness, reserved keys, geometry, labels, symbols, section presence, identity columns.
Fidelity: atom_id, per-direction fixed masks, and declared optional sections round-trip through the core reader/writer.
Campaigns: Pair with readcon-db (CON-text indexes, dedup, multi-reader; docs · docs.rs).
RPC: Cap'n Proto behind the rpc feature.

Migrate onto CON

Why switch: use a real frame API and multi-language library instead of hand-rolling XYZ and a private atoms object.

API: parse/write, builders, metadata, validation, compression, lazy multi-frame iteration
Payload: constraints, atom_id, optional sections, versioned JSON on one frame
Selection: select_atoms / rkr_frame_select (name H, bonds/angles when topology is present)
Languages: hourglass rkr_* in Fortran / C / C++ / Python / Julia / Rust (same semantics when you add a language)
Campaigns: readcon-db on CON text (energy / formula / sections, dedup, multi-reader; docs · docs.rs)
Plotting: chemparseplot (+ rgpycrumbs) on the same files
Measurements: Cachegrind I-refs; PR ASV + spyglass; peer scripts in benches/ — benchmarks.org

foreign → CON (needs --features chemfiles)

cargo run --release --features chemfiles -- convert structure.xyz structure.con

Python (readcon-chemfiles or maturin --features python,chemfiles)

python -c "import readcon; readcon.convert_to_con('structure.xyz','structure.con')"

How-to: docs/orgmode/migrate.org. Chemfiles path (CI-run): chemfiles-notebook. Campaigns: readcon-db docs · docs.rs/readcon-db. Plotting: chemparseplot.

Install

Language	Install	Destination
Rust	`cargo add readcon-core`	docs.rs
Python	`pip install readcon`	PyPI
Python + chemfiles	`pip install readcon-chemfiles`	PyPI
Campaign store	`cargo add readcon-db` / `pip install readcon-db`	docs · docs.rs
Julia	`julia --project=julia/ReadCon -e 'using Pkg; Pkg.instantiate()'`	bindings
C / C++ CMake	`FetchContent` / `find_package(readcon-core)` (cxx tarball)	headers + `libreadcon_core` + `readcon-core.pc`
C / C++ Meson	`dependency('readcon-core')` (wrapdb / wrap-file)	same
C / C++ cargo-c	`cargo cinstall --release --prefix /usr/local`	same

The C/C++ headers are shipped (include/readcon-core.h). cbindgen is a maintainer tool, not a consumer dependency. C99 (readcon-core.h) or C++17 (readcon-core.hpp) compiler. FetchContent URL: readcon-core-cxx-$VERSION.tar.gz on the GitHub Release. Full matrix: getting-started.

Tutorial

One Good Tutorial (Diátaxis): install, read a multi-frame fixture, inspect atom_id, write a round-trip, build a frame with energy. Full steps: docs/orgmode/tutorial.org (or the published HTML tutorial page).

Short Python path from the repository root:

import readcon

for frame in readcon.iter_con("resources/test/tiny_multi_cuh2.con"):
    print(frame.cell, len(frame), frame.energy)

frames = readcon.read_con("resources/test/tiny_multi_cuh2.con")
readcon.write_con("out.con", frames)

atoms = [readcon.Atom("Cu", 0.0, 0.0, 0.0, atom_id=0, mass=63.546)]
frame = readcon.ConFrame(cell=[10.0, 10.0, 10.0], angles=[90.0, 90.0, 90.0], atoms=atoms)
frame.set_energy(-42.5)
frame.write_con("built.con")

Rust smoke (same fixture):

cargo run --example rust_usage -- resources/test/tiny_multi_cuh2.con

Other languages and task recipes: docs/orgmode/howto.org. Conversion from XYZ/PDB/GRO: chemfiles-tutorial.

Design Decisions

Lazy parsing: ConFrameIterator parses one frame at a time for large trajectories.
Hourglass FFI: shipped C header plus a hand-written C++ RAII wrapper, same pattern as metatensor. CMake FetchContent, Meson wrap, and readcon-core.pc do not run cbindgen.

FFI Layer

Two exposure modes:

Opaque handles (RKRConFrame*): client calls Rust accessors (rkr_frame_get_header_line, …). Hides layout; ABI can evolve behind the handle.
Transparent #[repr(C)] extract (rkr_frame_to_c_frame → CFrame): client owns a flat atom table for hot loops and frees it with free_c_frame.

Specification

See docs/orgmode/spec.org (or the published HTML build) for the full specification. A summary follows.

CON format

A 9-line header (comments, cell dimensions, cell angles, atom type/count/mass metadata)
Line 2 is reserved for spec-v2 JSON metadata
Per-type coordinate blocks (symbol, label, atom lines with x y z fixed atomID)
Optional spec-v2 sections and validate metadata for declared per-atom sections and strict validation
Multiple frames are concatenated directly with no separator

convel format

Same as CON, with an additional velocity section after each frame's coordinates:

A blank separator line
Per-type velocity blocks (symbol, label, atom lines with vx vy vz fixed atomID)

Capabilities

Area	Surface
Payload	Constraints, `atom_id`; optional velocities / forces / energies / charges / spins / magmoms; versioned JSON
Languages	One `rkr_*` surface for Fortran / C / C++ / Python / Julia
Spec	v2–v3, `validate=true`, declared sections (including optional physics blocks above), units (v3)
Tensors	DLPack; optional metatensor `TensorBlock`
Campaigns	`index_proj` + readcon-db (docs · docs.rs)
Import	Optional chemfiles → CON
Measurements	Cachegrind I-refs; PR ASV + spyglass; `benches/compare_readers.py`

Predecessor: readCon.

Citation

If you use readcon-core in academic work, please cite it via the metadata in CITATION.cff. The Zenodo DOI tracks the latest release.

License

MIT.

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readcon-chemfiles 0.14.7

Table of Contents

About

Features

Migrate onto CON

foreign → CON (needs --features chemfiles)

Python (readcon-chemfiles or maturin --features python,chemfiles)

python -c "import readcon; readcon.convert_to_con('structure.xyz','structure.con')"

Install

Tutorial

Design Decisions

FFI Layer

Specification

CON format

convel format

Capabilities

Citation

License

Project links

Key dates

1 maintainer

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SHA256	`d5010028d5ea792a1f8c972d00bcd65ebfc17f226a0b5c90d4d68d3e93fc2c06`
MD5	`35645acae880d1480b048278709cc1f5`
BLAKE2b-256	`b52c7ff3d81d8b830d38cf9f750c9a91af6056bfae886035f7f65d006ad27ac1`

Algorithm	Hash digest
SHA256	`9141dd09aa630be43de6d3898ee999997936cb2bbbbf7d0bd61ee4d5a6b7440c`
MD5	`6afaeb20ba45064e49d1a453127669e4`
BLAKE2b-256	`1136f7fe9dd899eabb46cd9366fc094a7be42695e68b2742a476204abeb9542d`

Algorithm	Hash digest
SHA256	`047dc07a76e9364249846474b704579ec2d14561d247e9996d9a522bae1f122f`
MD5	`77969bb94b6a23c233c43d2aa7f5a70f`
BLAKE2b-256	`b03bec88a51a3c2a70f683802483d42d37d60ce0f202650fa5aa69238ba588e3`

Algorithm	Hash digest
SHA256	`ed6e954c1b7222189c84e2373eeb3ddf900cc28be8a2f28be06a2a215a8bd373`
MD5	`740cb3b2763333570cd448aa34bb7ca7`
BLAKE2b-256	`0826af8fc3f2a69dcb78eacc6578d1ddd04d690a5eb3627c7f0cc0d97518e6c3`

Algorithm	Hash digest
SHA256	`a58cff327ff8538fac2c01e0465c7411027c430134f154095da6fbca56e300c0`
MD5	`f1afa62a98806d21bd6b00bfbfd8ee1f`
BLAKE2b-256	`256b76df20df988ebd032f381ddc74afa6424be2827d689937d0a1c587c9766c`

Algorithm	Hash digest
SHA256	`8b745a8c78504d764e45a27965cdf05c6fc419026b8e6387fefc0441b8e939a4`
MD5	`42d3485e0129b10be99bf9d182ab654b`
BLAKE2b-256	`ee8afb8abd5d58bfcb0ab3f1128c3fb85e623afba7e7a7897f9cf141969280de`

Algorithm	Hash digest
SHA256	`a923737d3d9ee6d807ef37e69e598a78fa125bdcc128c6a4a5053c6c31e64635`
MD5	`057d3b21d1cc6b2d82578558f83f1623`
BLAKE2b-256	`35b9846cfdb5f79ee4d306362bb63e40b4fbb5236fe624822eea9983c38c4a13`

Algorithm	Hash digest
SHA256	`407c1075bf48f8d20a5531394257b8dc876b6beaf020068614db1be8b2b99c89`
MD5	`3e925a4bcbfd4b8b07ce9bb8fe30a3f2`
BLAKE2b-256	`b7731e6074d71efc67c65d5d40674d2888421cadd5c833c2cacf1baf10f21dfb`

Algorithm	Hash digest
SHA256	`76886a374e38b9ddabc63bfed4113401c0619051b36f0e251fb6e84ba6de605f`
MD5	`76ab74466ac62e3a25bd5c6db86447b8`
BLAKE2b-256	`38134884d09b90456a4aa462778412b8b96463df60a6bb44915dbac1a584d008`