# BioSim CZ MD Experiment metadata
#
# MD-specific metadata for an Experiment.  Referenced from experiment.yaml
# via the polymorphic `use:` directive.
#
# Fields are grouped into simulation setup, thermodynamic state, temporal
# extent, and system composition.
#
# Vocabulary references (type: vocabulary) are resolved via the registry in
# ./vocabularies/index.yaml.  Each `vocabulary-type:` identifier matches the stem
# of the corresponding definition file in ./vocabularies/.

MdMetadata:
  type: object
  properties:
    experiment_type:
      type: keyword
      required: true
      enum:
        - MD
      label:
        en: Experiment Type
      help:
        en: Discriminator for MD experiment metadata.

    simulation_setup:
      type: object
      label:
        en: Simulation Setup
      properties:
        software:
          type: vocabulary
          vocabulary-type: software
          label:
            en: Simulation Software
          help:
            en: Name of the MD engine (e.g., GROMACS, AMBER).

        software_version:
          type: keyword
          label:
            en: Software Version
          help:
            en: Version of the simulation software.

        force_field:
          type: vocabulary
          vocabulary-type: force_field
          label:
            en: Force Field
          help:
            en: >-
              Name of the force field used
              (e.g., CHARMM36, AMBER99SB-ILDN).

        water_model:
          type: vocabulary
          vocabulary-type: water_model
          label:
            en: Water Model
          help:
            en: Water model used in the simulation (e.g., TIP3P, SPC/E).

        integrator:
          type: vocabulary
          vocabulary-type: integrator
          label:
            en: Integrator
          help:
            en: Integrator algorithm (e.g., leap-frog, Verlet).

    thermodynamic_state:
      type: object
      label:
        en: Thermodynamic State
      properties:
        ensemble:
          type: vocabulary
          vocabulary-type: ensemble
          label:
            en: Ensemble
          help:
            en: Thermodynamic ensemble used in the simulation.

        reference_temperature:
          type: double
          min_inclusive: 0
          label:
            en: Reference Temperature (K)
          help:
            en: Reference temperature of the simulation in Kelvin.

        reference_pressure:
          type: double
          min_inclusive: 0
          label:
            en: Reference Pressure (bar)
          help:
            en: Reference pressure of the simulation (when applicable).

        thermostat:
          type: vocabulary
          vocabulary-type: thermostat
          label:
            en: Thermostat
          help:
            en: >-
              Temperature coupling algorithm
              (e.g., V-rescale, Nosé-Hoover).

        barostat:
          type: vocabulary
          vocabulary-type: barostat
          label:
            en: Barostat
          help:
            en: >-
              Pressure coupling algorithm
              (e.g., Parrinello-Rahman, Berendsen).

    temporal_extent:
      type: object
      label:
        en: Temporal Extent
      properties:
        simulation_length:
          type: double
          min_exclusive: 0
          label:
            en: Simulation Length (ns)
          help:
            en: Total simulated time in nanoseconds.

        timestep:
          type: double
          min_exclusive: 0
          label:
            en: Timestep (fs)
          help:
            en: Integration timestep in femtoseconds.

        number_of_steps:
          type: long
          min_exclusive: 0
          label:
            en: Number of Steps
          help:
            en: Total number of integration steps.

    system:
      type: object
      label:
        en: System
      properties:
        total_atoms:
          type: long
          min_exclusive: 0
          label:
            en: Total Atoms
          help:
            en: Total number of atoms in the simulated system.

        box_type:
          type: vocabulary
          vocabulary-type: box_type
          label:
            en: Box Type
          help:
            en: Simulation box geometry (e.g., cubic, dodecahedron, octahedron, triclinic).

        box_dimensions:
          type: array
          min_items: 3
          max_items: 6
          label:
            en: Box Dimensions
          help:
            en: >-
              Box lengths (a, b, c) and, if applicable,
              angles (alpha, beta, gamma).
          items:
            type: double
            min_exclusive: 0