Molecular Dynamics support

Molecular dynamics calculations do not currently have any meaningful representation in the overview. The archive has metainfo for capturing at least part of MD information, but it's not currently referenced/copied to results. The concepts we create and apply for molecular dynamics data will also need to be applied to other data originating from complex workflows (e.g. geometry optimization).

Data

• Create a small dataset of typical, simple MD runs from software for which we have parsers for. Should include both classical MD and quantum MD.

Metainfo

• All relevant MD properties should be stored directly under run.calculation. This requires moving some quantities around (e.g. from run.calculation.thermodynamics)
• Add new metainfo for keeping track of the simulation time (calculation.time) and simulation time step (calculation.step)
• Rethink the layout for results.properties: we should not have separate sections for all kinds of different workflows (e.g. currently we have a section for results.properties.geometry_optimization). Instead, we should think in terms of what physical properties are extracted from these workflows and then distribute them into suitable categories (e.g. mechanical, electronic, thermodynamic, etc.). This way we can create an easily navigatable hierarchy where the same properties are not found in several locations (e.g. radial distribution function from MD vs. radial distribution function from experiment should be found in the same place.)
• Each property should be able to also carry extra information related to the methodology that was used for calculating it. This methodology should hold e.g. sampling settings, thresholds etc. that DO NOT affect the energetics of the system (results.method holds the actual physical model details that also affect the energetics). As an example of this, we should store the MD settings (timestep, thermostat, barostat etc.) under the properties extracted from MD.

Parsers

• Adjust the relevant parsers so that they output MD properties correctly using the new data layout.

Normalizing

• The results normalizer should extract MD information from an MD workflow section and store it under results.

GUI

• Overview:
  • Plots for all thermodynamical properties
  • Ensemble type and timestep
• Search:
  • Ensemble type
  • Timestep
  • Present thermodynamical properties: temperature, pressure volume and potential energy to begin with.