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REMORA_Fennel_Fortran_Interface.H File Reference
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Go to the source code of this file.
Function Documentation
◆ fennel_bridge_advance_c()
| void fennel_bridge_advance_c | ( | int | ilo, |
| int | ihi, | ||
| int | jlo, | ||
| int | jhi, | ||
| int | nz, | ||
| int | nbt, | ||
| int | istr, | ||
| int | iend, | ||
| int | jstr, | ||
| int | jend, | ||
| int | use_po4, | ||
| int | use_carbon, | ||
| int | use_oxygen, | ||
| int | use_odu, | ||
| int | use_denit, | ||
| int | use_biosed, | ||
| int | use_bulk, | ||
| int | use_rivdon, | ||
| int | use_talknc, | ||
| int | pco2air_kind, | ||
| int | co2_sc_kind, | ||
| int | o2_sc_kind, | ||
| int | bioiter, | ||
| double | dt_sec, | ||
| double | rho0, | ||
| double | cp_heat, | ||
| double | p_AttSW, | ||
| double | p_AttChl, | ||
| double | p_PARfrac, | ||
| double | p_Vp0, | ||
| double | p_I_thNH4, | ||
| double | p_D_p5NH4, | ||
| double | p_NitriR, | ||
| double | p_K_NO3, | ||
| double | p_K_NH4, | ||
| double | p_K_PO4, | ||
| double | p_K_Phy, | ||
| double | p_Chl2C_m, | ||
| double | p_ChlMin, | ||
| double | p_PhyCN, | ||
| double | p_R_P2N, | ||
| double | p_PhyIP, | ||
| double | p_PhyIS, | ||
| double | p_PhyMin, | ||
| double | p_PhyMR, | ||
| double | p_ZooAE_N, | ||
| double | p_ZooCN, | ||
| double | p_ZooBM, | ||
| double | p_ZooER, | ||
| double | p_ZooGR, | ||
| double | p_ZooMin, | ||
| double | p_ZooMR, | ||
| double | p_LDeRRN, | ||
| double | p_LDeRRC, | ||
| double | p_CoagR, | ||
| double | p_SDeRRN, | ||
| double | p_SDeRRC, | ||
| double | p_RDeRRN, | ||
| double | p_RDeRRC, | ||
| double | p_wPhy, | ||
| double | p_wLDet, | ||
| double | p_wSDet, | ||
| double | p_pCO2air, | ||
| const double * | rmask, | ||
| const double * | Hz, | ||
| const double * | z_r, | ||
| const double * | z_w, | ||
| const double * | srflx, | ||
| const double * | sustr, | ||
| const double * | svstr, | ||
| const double * | uwind, | ||
| const double * | vwind, | ||
| double * | pH, | ||
| const double * | t_nstp, | ||
| double * | t_nnew, | ||
| int | dbg_level, | ||
| int | dbg_i, | ||
| int | dbg_j | ||
| ) |
C interface to the ROMS Fennel kernel (Path A oracle).
Wraps biology_tile from the tracked copy of ROMS fennel.h. See Source/Biology/Fortran/REMORA_fennel_roms.F for the isohelper and Source/Biology/Fortran/tag_map.md for the diagnostic contract.
- Note
- All arrays are contiguous packed buffers owned by the caller, in Fortran (column-major, i fastest) order. Nothing is aliased directly from an AMReX FArrayBox: REMORA FABs carry ghost cells and a 0-based k index, while ROMS wants 1-based k over the valid region, so the pack/unpack is explicit and lives in REMORA_FennelBridge.cpp.
- Storage bounds (ilo..ihi, jlo..jhi, nz) and active bounds (istr..iend, jstr..jend) are passed separately, matching the ROMS memory-extent versus compute-extent distinction.
- i and j are REMORA's own 0-based indices; the Fortran side sets its array lower bounds to match, so no horizontal index translation happens anywhere. Only k is shifted (REMORA k -> ROMS k+1), by the packer.
Array shapes, in Fortran notation: rmask, srflx, uwind, vwind, pH (ilo:ihi, jlo:jhi) sustr, svstr (ilo:ihi+1, jlo:jhi+1) Hz, z_r (ilo:ihi, jlo:jhi, 1:nz) z_w (ilo:ihi, jlo:jhi, 0:nz) t_nstp, t_nnew (ilo:ihi, jlo:jhi, 1:nz, 1:nbt+2)
The tracer dimension is ROMS-ordered: index 1 is temperature, 2 is salinity, 3.. are the biology tracers in Fennel order. That equals the REMORA component index plus one throughout.
- Parameters
-
nbt biology tracer count; validated against the compiled ROMS option set, which aborts the run on mismatch dt_sec full baroclinic step in seconds (NOT divided by BioIter; the ROMS kernel does that division itself) rho0 reference density, for the ROMS kinematic-srflx conversion PARsur = PARfrac*srflx*rho0*Cp cp_heat seawater specific heat, same conversion pH inout for interface fidelity; write-only in practice, since fennel.h fixes DoNewton = 0 and the bisection brackets are constants dbg_level 0 off, 1 target column, 2 all columns
