Wiki¶
Process, worked examples, and the 2020 SQM notes. The product page is dseams.info. API books:
- Engine and
seamsCLI: docs.dseams.info - Python
Frame: pydseams - Lua
require("dseams"): yodaStruct - PLUMED action: dseams-plumed
Cite the 2020 paper (DOI 10.1021/acs.jcim.0c00031, arXiv:1909.09830).
Trajectories: figshare project 73545. Records: Zenodo community.
Examples¶
These pages use the 2.7 public API. seams covers read, chill, chill-plus, cages --graph seeded --complete, fingerprint, ions, rdf, cn, hbonds, pairs, density-z, and domains. pydseams adds Frame.from_file / from_ase / from_arrays, fingerprint, ion_environment, and IceFeaturizer. Lua is require("dseams"). Collective variables use DSEAMS_CAGES. The 2020 YAML / yodaStruct -c driver is gone.
ds.read remains a documented suffix-dispatch alias; new examples call Frame.from_file for LAMMPS dumps.
- seams CLI
- CHILL+ on a cubic lattice
- Bulk HC / DDC cages
- Topology fingerprint
- Ions against cages
- Ice features
- Visualise labels
- PLUMED DSEAMS_CAGES
- Ice nanotube prisms
- Monolayer square ice
- In-plane RDF
Python and Lua libraries¶
The Python distribution is pydseamslib and its import is pydseams. The Lua module is require("dseams"); require("yoda") is a compatibility alias. Both libraries call the native engine and expose trajectory reading, CHILL/CHILL+, cages, fingerprints, ion environments, radial distributions, coordination numbers, hydrogen bonds, density profiles, ionic pairs, and domain statistics.
Use the generated books for the live names:
Process¶
The SQM plan is the 2020 Software Quality Management course artifact. Keep it as history.