Models (model.yaml)

# ModelSpec: code refs, template refs, bgc_mode, and model-specific physics/numerics
# defaults.
#
# This intentionally holds nothing that a Domain/Forcing/Output spec already provides:
# no grid/IC/forcing source selection (that's a ForcingSpec's job -- pick one from the
# catalog; there is no more "model default" forcing) and no ocean_vars/surf_flux/
# diagnostics/stdout_diag/ts_output/frc_output/cdr_output/upscale_output/zslice/
# random_output sections or marbl_bgc write-lists (those are an OutputSpec's job -- pick
# one from the catalog; there is no more "model default" output either). Nor does it
# hold anything Domain-owned (open_boundaries -> cppdefs.obc_*; grid_kwargs/
# partitioning -> param's llm/mmm/n/np_xi/np_eta) or Forcing-owned (tidal presence ->
# cppdefs.tides + tides.ntides; MBL_co2 surface item -> cppdefs.co2_tvarying;
# restoring surface forcing with an SSS component -> cppdefs.sal_restore;
# river_frc/cdr_frc namelist defaults, which the resolver now owns directly and a
# ForcingSpec may override -- see build_forge_blueprint). Nor does it hold
# extract_data (child-grid nesting): its active values come from a second,
# separately-selected DomainSpec (the nesting child), so the resolver owns its
# disabled fallback directly too.
#
# `bgc_mode` (marbl|none) is a per-run toggle: it prepopulates the wizard's BGC
# dropdown and the resolver uses it to set cppdefs.marbl (and gate nhy_forcing/
# nox_forcing) and to decide whether code.marbl is populated.
#
# `use_pio` (bool) is a per-run toggle mirroring bgc_mode: it prepopulates the
# wizard's PIO checkbox and the resolver uses it to set cppdefs.use_pio and to
# decide whether code.pio is populated.
#
# `model_settings` is flat and mirrors ForgeBlueprint.model_settings 1:1 (cppdefs sits
# at the same level as the namelist sections, matching how the resolver treats them).
# A few sections here are fully overwritten by the resolver at build time regardless of
# what's written below (time_stepping, v_sponge from grid/run-window; param's
# llm/mmm/n/np_xi/np_eta from grid/partitioning; cppdefs.obc_*/marbl/co2_tvarying/
# sal_restore/tides/cdr_forcing/use_pio from, respectively, open boundaries/bgc_mode/
# forcing selection/forcing selection/tidal-forcing presence/CDR-forcing presence/the
# top-level use_pio toggle; river_frc/cdr_frc entirely; extract_data
# entirely; tides.ntides from tidal forcing) -- they're included
# below only where the remaining fields in that same section (cppdefs' sponge_tune/
# nhy_forcing/nox_forcing; param's nt_passive/ntrc_bio; tides' bry_tides/pot_tides/
# ana_tides) are real, still-relevant model defaults. `pipe_frc` stays here in full:
# there is no pipe forcing item or generation path, so it has no other spec to
# live in.

bgc_mode: marbl  # marbl|none -- prepopulates the wizard; resolver derives cppdefs.marbl from it
use_pio: false  # prepopulates the wizard's PIO checkbox; resolver derives cppdefs.use_pio from it

code:
  roms:
    location: https://github.com/CWorthy-ocean/ucla-roms.git
    commit: 0.2.0

  marbl:
    location: https://github.com/CWorthy-ocean/MARBL.git
    commit: marbl0.45.0-max-it-10

  pio:
    location: https://github.com/CWorthy-ocean/ParallelIO.git
    commit: 2.7.1-fork

  # Render templates live at the forge repo root (templates/), decoupled from this
  # ModelSpec: they track a ROMS version, change infrequently, and may move into the
  # ucla-roms repo later. `directory` is relative to the repo root. At processing time
  # the executor fetches these via C-Star's AdditionalCode from the forge git ref.
  # Pin the serving forge commit with `templates_commit:` (until pinned, the resolver
  # defaults to branch `main`).
  templates_commit: 692e04cebf1735951b377fcf44b1bde59a06bbc9
  templates_compile_time:
    directory: "templates/compile-time"
    files:
    - cppdefs.opt.j2
  templates_run_time:
    directory: "templates/run-time"
    files:
    - marbl_in

model_settings:
  cppdefs:
    # obc_west/east/north/south, marbl, co2_tvarying, sal_restore, tides, cdr_forcing,
    # and use_pio are all resolver-derived (from the domain's open_boundaries, bgc_mode,
    # forcing selection, restoring-forcing SSS component, tidal-forcing presence,
    # CDR-forcing presence, and the top-level use_pio toggle, respectively) and are
    # intentionally absent here -- there is no separate cppdefs-level default to
    # duplicate (use_pio's own default lives at the top level, above). auto_tiling is
    # also fully resolver-derived (from partitioning["auto_tiling"], no ModelSpec-level
    # fallback) but is declared below anyway, mirroring sponge_tune/nhy_forcing/
    # nox_forcing, so the schema documents its default inline.
    sponge_tune: false  # advanced setting only (nested-domain pressure flux forcing); not resolver-derived
    nhy_forcing: true  # ammonia atmospheric forcing; forced off by the resolver when bgc_mode="none"
    nox_forcing: true  # nitrogen oxide atmospheric forcing; forced off by the resolver when bgc_mode="none"
    auto_tiling: false  # MPI_MASKING (ucla-roms 0.5.0); resolver always overwrites this from partitioning["auto_tiling"]

  lateral_visc:
    visc2: 0.0  # m^2/sec
    rho0: 1000.0

  vertical_mixing:
    akv: 0.0  # m^2/sec
    # akt is a list of values, one per tracer (NT tracers)
    # Default is all zeros - will be generated in template
    akt_default: 0.0

  tracer_diff2:
    # tnu2 is a list of values, one per tracer (NT tracers)
    # Default is all zeros - will be generated in template
    tnu2_default: 0.0

  bottom_drag:
    rdrg: 0.0E-4  # m/s
    rdrg2: 1.0E-3
    zob: 1.0E-2  # meters

  gamma2: 1.0  # Slipperiness parameter

  ubind: 0.1  # m/s, OBC binding velocity scale

  param:
    # llm/mmm/n/np_xi/np_eta are Domain-owned (resolver-derived from grid_kwargs/
    # partitioning) and intentionally absent here; nsub_x/nsub_e are hardcoded by the
    # resolver. Only nt_passive/ntrc_bio (real model-level BGC tracer counts) live here.
    nt_passive: 0
    ntrc_bio: 32

  # Output-write-control fields (wrt_*/output_period_*/nrpf_*) are an OutputSpec's
  # job (Output.yaml's own `bgc:` block) and are deep-merged on top of these at
  # resolve time -- only the physics defaults stay here.
  bgc:
    nbgc_flx: 2
    interp_frc: 0
    xco2air_default: 284.7  # Atmospheric xCO2 (ppm) when PCO2AIR_FORCING is off

  blk_frc:
    interp_frc: 0
    check_bulk_frc_units: false

  tides:
    # ntides is Forcing-owned (set by the resolver from the tidal item's ntides, or 0
    # when there is no tidal forcing) and intentionally absent here.
    bry_tides: true
    pot_tides: true
    ana_tides: false

  sponge_tune:
    pflx_w_vname: 'up_west'
    pflx_w_tname: 'bry_time'
    pflx_e_vname: 'up_east'
    pflx_e_tname: 'bry_time'
    pflx_s_vname: 'vp_south'
    pflx_s_tname: 'bry_time'
    pflx_n_vname: 'vp_north'
    pflx_n_tname: 'bry_time'
    ub_tune: false
    spn_avg: true
    sp_timscale: 86400  # 24*3600 seconds
    wrt_sponge: false
    nrpf: 7
    output_period: 86400  # 24*3600 seconds

  flux_frc:
    interp_flux_frc: true

  # calc_pflx absorbs diag_pflx and its timescale from the old diagnostics.opt
  calc_pflx:
    calc_pflx: true
    timescale: 86400  # timescale for filtering pressure fluxes (s)

  pipe_frc:
    pipe_source: false
    p_analytical: false
    npip: 1

  particles:
    floats: false
    np: 50
    extra_space_fac: 1.5
    exchange_facx: 0.1
    exchange_facy: 0.1
    exchange_facc: 0.01
    output_period: 400
    nrpf: 100
    ppm3: 1.0e-6
    pmin: 200

  lin_rho_eos:
    tcoef: 0.2    # Thermal expansion coefficient (kg/m2/K); unused if NONLIN_EOS active
    t0: 1.0       # Reference temperature (*C)
    scoef: 0.822  # Saline contraction coefficient (kg/m3/psu)
    s0: 1.0       # Reference salinity (psu)

  sss_correction:
    dsssdt: 7.777  # SSS correction piston velocity (cm/day); requires SFLX_CORR + SALINITY

  sst_correction:
    dsstdt: 7.777  # SST correction piston velocity (cm/day); requires QCORRECTION

  dic_alk_correction:
    dcdt: 7.777  # DIC/ALK correction piston velocity (cm/day); requires CFLX_CORR + MARBL

  marbl_bgc:
    marbl_config_file: "marbl_in"
    marbl_timestep: 3600.0
    # marbl_tracers_to_write / marbl_diagnostics_to_write are OutputSpec's (see Output.yaml)

description: ucla-roms main + PIO enabled
bgc_mode: marbl
use_pio: true
code:
  roms:
    location: https://github.com/CWorthy-ocean/ucla-roms.git
    commit: main
  marbl:
    location: https://github.com/CWorthy-ocean/MARBL.git
    commit: marbl0.45.0-max-it-10
  pio:
    location: https://github.com/CWorthy-ocean/ParallelIO.git
    commit: 2.7.1-fork
  templates_commit: 692e04cebf1735951b377fcf44b1bde59a06bbc9
  templates_compile_time:
    directory: templates/compile-time
    files:
    - cppdefs.opt.j2
  templates_run_time:
    directory: templates/run-time
    files:
    - marbl_in
model_settings:
  cppdefs:
    sponge_tune: false
    nhy_forcing: true
    nox_forcing: true
    auto_tiling: false
  lateral_visc:
    visc2: 0.0
    rho0: 1000.0
  vertical_mixing:
    akv: 0.0
    akt_default: 0.0
  tracer_diff2:
    tnu2_default: 0.0
  bottom_drag:
    rdrg: 0.0
    rdrg2: 0.001
    zob: 0.01
  gamma2: 1.0
  ubind: 0.1
  param:
    nt_passive: 0
    ntrc_bio: 32
  pio_settings:
    pio_stride: 1  # PIO I/O-task rank stride; unread by ucla-roms releases predating the PIO_SETTINGS namelist group
  bgc:
    nbgc_flx: 2
    interp_frc: 0
    xco2air_default: 284.7
  blk_frc:
    interp_frc: 0
    check_bulk_frc_units: false
  tides:
    bry_tides: true
    pot_tides: true
    ana_tides: false
  sponge_tune:
    pflx_w_vname: up_west
    pflx_w_tname: bry_time
    pflx_e_vname: up_east
    pflx_e_tname: bry_time
    pflx_s_vname: vp_south
    pflx_s_tname: bry_time
    pflx_n_vname: vp_north
    pflx_n_tname: bry_time
    ub_tune: false
    spn_avg: true
    sp_timscale: 86400
    wrt_sponge: false
    nrpf: 7
    output_period: 86400
  flux_frc:
    interp_flux_frc: true
  calc_pflx:
    calc_pflx: true
    timescale: 86400
  pipe_frc:
    pipe_source: false
    p_analytical: false
    npip: 1
  particles:
    floats: false
    np: 50
    extra_space_fac: 1.5
    exchange_facx: 0.1
    exchange_facy: 0.1
    exchange_facc: 0.01
    output_period: 400
    nrpf: 100
    ppm3: 1.0e-06
    pmin: 200
  lin_rho_eos:
    tcoef: 0.2
    t0: 1.0
    scoef: 0.822
    s0: 1.0
  sss_correction:
    dsssdt: 7.777
  sst_correction:
    dsstdt: 7.777
  dic_alk_correction:
    dcdt: 7.777
  marbl_bgc:
    marbl_config_file: marbl_in
    marbl_timestep: 3600.0