d-SEAMS

Author:

d-SEAMS core team

Read

Load a LAMMPS frame and print nop, frame, and box.

Quickstart
Classify

CHILL+ four-neighbour star: cubic, hexagonal, interfacial, water.

Classify ice on the mixed TIP4P example
Score

Cage membership: HC is ice Ih, DDC is ice Ic, else water.

CHILL+ versus cages

Overview

d-SEAMS (Deferred Structural Elucidation Analysis for Molecular Simulations) classifies ice in molecular-dynamics trajectories. This repository is the C++ engine (libyodaLib) and the seams CLI.

seams read water.lammpstrj
seams chill-plus water.lammpstrj --cutoff 3.5
seams cages water.lammpstrj

Scripting front ends are separate packages:

The header Ecosystem menu on every page jumps between the engine, the bindings, and linkcell.

Build with a Nix flake (nix build, nix develop) or with pixi run setup && pixi run build && pixi run test.

Suite stack

        flowchart TB
  subgraph engine["seams-core"]
    LIB[libyodaLib]
    CLI[seams CLI]
  end
  subgraph fronts["Front ends"]
    PY[pydseams Frame]
    LUA["require(\"dseams\")"]
  end
  LC[linkcell]
  DUMP[LAMMPS / XYZ / chemfiles / con] --> LIB
  LC --> LIB
  LIB --> CLI
  LIB --> PY
  LIB --> LUA
  CLI --> OUT[stdout counts]
  PY --> ASE[ASE / solvis extras]

Documentation structure

This documentation follows the Diataxis framework.

Getting Started

Tutorials

How-to

Explanation

Reference

Development

License

MIT. Cite the 2020 JCIM paper (DOI 10.1021/acs.jcim.0c00031). See Citation.