2026-10-14 MD analysis: H5MD output, a shared library and analysis steps

Goal

Bring the analysis that the science and mlff sessions now do in their own scripts into SEAMM: viscosity, diffusion constants with the Yeh–Hummer correction, the dielectric constant, radial distribution functions, coordination and ion pairing, with honest error bars and the results stored as SEAMM properties.

The design rests on three parts:

1. one H5MD file written by each MD step, holding its trajectory and time series;

2. a shared analysis library that the analysis steps are built on;

3. analysis steps that either run their own MD replicas or analyse the MD that came before them in the flowchart.

The data contract does not depend on the MD code, so a GROMACS step can feed the same analysis steps later.

The discussion behind it, 2026-10-14, is in Paul’s notes for that day. The decisions are summarized in the design document.

Contents:

• The design
  • Decisions already made
  • Where things stand
  • H5MD facts checked on 2026-10-14
  • Overview
  • The data contract: SEAMM’s H5MD layout
  • How analysis finds the data: _md_runs
  • Requirements and catching mistakes before the MD runs
  • Two modes for each analysis step
  • The shared library: seamm_md_analysis
  • The LAMMPS step
  • The analysis steps
  • Non-periodic systems
  • GROMACS later
  • Phases
  • Validation
  • Open questions
• Phase 5: extra commands and extra properties in the MD sub-steps
  • Goal
  • Where it goes in the code
  • 1. The parameters
  • 2. The input
  • 3. Units
  • 4. Treatments
  • 5. Storage and results
  • 6. The GUI
  • 7. Tests
  • 8. Releases
  • Decisions (Paul, 2026-10-16)
  • The questions as they were put
• Phase 6: the structure of liquids and solutions
  • Goal
  • 1. The step
  • 2. What to analyse: species and sites
  • 3. Radial distribution functions and coordination numbers
  • 4. Ion pairing
  • 5. Solvation shells and residence times (SolvationAnalysis)
  • 6. Results
  • 7. Non-periodic systems
  • 8. Dependencies and memory
  • 9. Tests
  • 10. Releases
  • Revision (Paul, 2026-10-16, during implementation)
  • Decisions (Paul, 2026-10-16: the recommendations below)