Deferred Structural Elucidation Analysis for Molecular Simulations

Classify ice in MD trajectories.

Version 2.9.0 is the seams-core engine and the seams CLI. Python, Lua, PLUMED, and linkcell live in their own repositories. 2.x has an expanded team.

Read the docs seams-core

2.x

One engine. Named packages.

Users install the public names below. Install and API detail live on docs.dseams.info and the binding books.

1.x / 2020

One yodaStruct executable. YAML plus Lua. JCIM paper.

2.x

seams CLI from seams-core v2.9.0. pydseamslib on PyPI, with an MDAnalysis analysis, an OVITO modifier and a Colab notebook. yodaStruct for Lua and Fennel. dseams-plumed for DSEAMS_CAGES. linkcell for periodic kNN.

Elja exclusive Xeon Platinum 8358, job 1785712. Base `1c8efa3` vs tip `13c95ce`. Times in ms, best-of. Manifest: `repro/reference/paper_manifest-elja-1785712.json`.
Stage	N	1.x scan	2.x
neighbour list	32000	862.2	43.5
ring index	32000	5955.5	42.4
CHILL+	32000	111.5	44.8
six-rings	4096	100.7	13.9
findHC	4096	3582.9	45.2

The suite

seams-core

v2.9.0. The seams CLI on the C++ engine: cages, CHILL+, topology keys, ions, guests, and per-atom dumps for OVITO or VMD.

docs
pydseamslib

v2.9.0. pip install pydseamslib; import pydseams. Frame API, features for deeptime and PyEMMA, ion and guest helpers, pydseams.adapters for MDAnalysis and OVITO.

book
yodaStruct

v2.9.0. Lua and Fennel. require("dseams").

book
dseams-plumed

v0.3.0. The DSEAMS_CAGES PLUMED action: cage counts, ion classes, key libraries and filled cages on the fly.
linkcell

Periodic linked-cell k-nearest neighbours for Rust, C, C++, and Python.
readcon-core

CON input. Repository: lode-org/readcon-core.

Repositories

Eight repositories live under github.com/d-SEAMS: seams-core, PydSEAMSlib, yodaStruct, linkcell, dseams-plumed, dseams2_repro, wiki and landing. The CON reader the engine embeds, readcon-core, lives with its LODE siblings under lode-org.

d-SEAMS/seams-core engine and seams CLI
d-SEAMS/PydSEAMSlib Python binding
d-SEAMS/yodaStruct Lua and Fennel
d-SEAMS/linkcell periodic kNN crate
d-SEAMS/wiki process and examples
d-SEAMS/landing this site
d-SEAMS/dseams-plumed DSEAMS_CAGES
d-SEAMS/dseams2_repro reproducibility package
lode-org/readcon-core CON input

Call it

Install the Python wheel with pip install pydseamslib; the import remains pydseams. The seams CLI commands are read, chill, chill-plus, cages, fingerprint, ions, rdf, cn, hbonds, pairs, density-z, and domains.

CLI

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

Python

import pydseams as ds
frame = ds.read("water.lammpstrj")
print(frame.chill_plus())
print(frame.cages())

Lua

local dseams = require("dseams")
local cloud = dseams.read("water.lammpstrj")
print(dseams.chill_plus(cloud, {cutoff = 3.5}))

Two classifiers

CHILL+

Four-neighbour star. Labels cubic, hexagonal, interfacial, clathrate, and water. It does not assign cage membership.

Cages

Hexagonal cages (HC) are ice Ih. Double-diamond cages (DDC) are ice Ic. Everything else is water on that score.

Cubic, hexagonal, and interfacial ice forming on a surface — Ic, Ih, and interfacial ice on a surface.

Hexagonal ice as a topological ring network — Pure hexagonal ice as a ring network.

Radial distribution plots of a bulk system at several temperatures — Radial distribution of a bulk system at several temperatures.

Lua modules loaded without recompilation — Lua modules without recompilation.

Demos

1.x

The published nix install of the single yodaStruct binary.

2.x

The 2.x recording runs seams cages, pip install pydseamslib with import pydseams, and require("dseams"). The package books document each complete API.

1.x recording

2.x recording

Download the 2.x recording

Cite

Goswami, R.; Goswami, A.; Singh, J. K. d-SEAMS: Deferred Structural Elucidation Analysis for Molecular Simulations. J. Chem. Inf. Model. 2020. 10.1021/acs.jcim.0c00031 / arXiv:1909.09830

Software 2.x authors are listed in each package's CITATION.cff. The reproducibility package is dseams2_repro.