prod.wic

# Use &filename to create a reference to an output. Inputs in later steps can
# use *filename to dereference the filename and create an explicit edge.
inputs:
  nsteps:
    type: int
  dt:
    type: float
  ref-t:
    type: float
  ref-p:
    type: float

steps:
    config_tag_mdp:
      in:
        nsteps: nsteps #10000
        dt: dt #0.002
        ref-t: ref-t #298.0
        ref-p: ref-p #1.0
        config: !ii
          mdp:
            integrator: md  # Use md for performance so we can update coordinates on GPU. Use sd for proper statistical properties.
            rvdw: 1.0
            rcoulomb: 1.0
            coulombtype: PME
            tc-grps: system
            tau-t: 2
            constraints: h-bonds
            nstxout: 1000
            nstenergy: 1000
            pcoupl: Parrinello-Rahman
            tau-p: 1
            compressibility: 4.5e-5
            comm-mode: Linear
            comm-grps: system
      out:
      - output_config_string: !& config_tag_mdp_prod
    grompp:
      in:
        config: !* config_tag_mdp_prod
        input_top_zip_path: !* genion.zip  # Use the original topology file so
# we don't have to question whether the topology gets messed up after file format conversions.
# (In fact, it is not exactly identical!)
      out:
      - output_tpr_path: !& prod.tpr
    mdrun:
      in:
        output_trr_path: !ii prod.trr # Explicitly specify for cwl_subinterpreter
      out:
      - output_crd_path: !& prod.gro
      - output_trr_path: !& prod.trr
      - output_edr_path: !& prod.edr
  # - cwl_subinterpreter_analysis.wic:

wic:
  graphviz:
    label: Production
  steps:
    (1, config_tag_mdp):
      wic:
        graphviz:
          label: 'Configure Default\nGromacs Options'
    (2, grompp):
      wic:
        graphviz:
          label: 'Update\nTopology'
    (3, mdrun):
      wic:
        namespace: gpu  # To run MD on GPU
        graphviz:
          label: 'Molecular\nDynamics'
    (4, cwl_subinterpreter_analysis.wic):
      wic:
        implementation: protein
        graphviz:
          label: 'Real-time\nAnalysis'
          style: invis # Make this node invisible