├── .git_filters ├── id.clean └── id.smudge ├── .gitattributes ├── CMakeLists.txt ├── Compilers ├── AIX-xlf.mk ├── CYGWIN-df.mk ├── CYGWIN-g95.mk ├── CYGWIN-gfortran.mk ├── CYGWIN-ifort.mk ├── Darwin-f90.mk ├── Darwin-gfortran.mk ├── Darwin-ifort.mk ├── Darwin-nag.mk ├── Darwin-pgi.mk ├── Darwin-xlf.mk ├── FindESMF.cmake ├── IRIX64-f90.mk ├── Linux-ftn-cray.mk ├── Linux-ftn-gnu.mk ├── Linux-ftn-intel.mk ├── Linux-ftn.mk ├── Linux-g95.mk ├── Linux-gfortran.mk ├── Linux-ifc.mk ├── Linux-ifort.mk ├── Linux-ifx.mk ├── Linux-necsx.mk ├── Linux-path.mk ├── Linux-pgi.mk ├── MINGW-g95.mk ├── MINGW-gfortran.mk ├── Makefile.cice ├── OSF1-f90.mk ├── SunOS-f95.mk ├── SunOS-ftn.mk ├── UNICOS-mk-f90.mk ├── UNICOS-mp-ftn.mk ├── UNICOS-sn-f90.mk ├── compiler_flags_GNU_Fortran.cmake ├── compiler_flags_Intel_Fortran.cmake ├── defs_cmake.h ├── make_macros.h ├── my_build_paths.csh ├── my_build_paths.sh ├── roms_compiler_flags.cmake ├── roms_config.cmake └── roms_functions.cmake ├── Data └── ROMS │ └── CDL │ ├── README.md │ ├── adsen.cdl │ ├── bry_limit.cdl │ ├── bry_unlimit.cdl │ ├── clm_ts.cdl │ ├── frc_bulk.cdl │ ├── frc_fluxclm.cdl │ ├── frc_respiration.cdl │ ├── frc_rivers.cdl │ ├── frc_tides.cdl │ ├── frc_uvstress.cdl │ ├── grd_spherical.cdl │ ├── ini_ecosim.cdl │ ├── ini_fennel.cdl │ ├── ini_hydro.cdl │ ├── ini_sed.cdl │ ├── nesting.cdl │ ├── nudgcoef.cdl │ ├── s4dvar_obs.cdl │ ├── s4dvar_std_b.cdl │ ├── s4dvar_std_f.cdl │ ├── s4dvar_std_i.cdl │ └── s4dvar_std_m.cdl ├── ESM ├── Readme.md ├── build_cice.csh ├── build_ufs.csh ├── build_ufs.sh ├── build_wps.csh ├── build_wps.sh ├── build_wrf.csh ├── build_wrf.sh ├── coamps_explicit.runconfig ├── coamps_implicit.runconfig ├── coamps_implicit_wildcard.runconfig ├── coupling_esmf.in ├── coupling_esmf.yaml ├── coupling_esmf_coamps.yaml ├── coupling_esmf_wrf.yaml ├── data.runconfig ├── data_snapshots.runconfig ├── esm_libs.csh ├── esm_libs.sh ├── roms_cmeps.yaml ├── roms_test_ufs.sh ├── wrf_explicit.runconfig ├── wrf_implicit.runconfig ├── wrf_links.csh ├── wrf_links.sh ├── wrf_move.csh └── wrf_move.sh ├── License_ROMS.md ├── Master ├── CMakeLists.txt ├── Module.mk ├── cmeps_roms.h ├── coupler.F ├── esmf_atm.F ├── esmf_atm_coamps.h ├── esmf_atm_regcm.h ├── esmf_atm_void.h ├── esmf_atm_wrf.h ├── esmf_coupler.h ├── esmf_data.F ├── esmf_driver.h ├── esmf_esm.F ├── esmf_ice.F ├── esmf_ice_cice.h ├── esmf_ice_void.h ├── esmf_roms.F ├── esmf_roms.h ├── esmf_wav.F ├── esmf_wav_void.h ├── esmf_wav_wam.h ├── master.F ├── mct_coupler.h ├── mct_driver.h ├── mct_roms_swan.h ├── mct_roms_wrf.h ├── mod_esmf_esm.F ├── propagator.F ├── roms.h └── roms_kernel.F ├── ROMS ├── Adjoint │ ├── Biology │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── ad_biology.F │ │ ├── ad_npzd_Franks.h │ │ ├── ad_npzd_Powell.h │ │ └── ad_npzd_iron.h │ ├── CMakeLists.txt │ ├── Module.mk │ ├── ad_balance.F │ ├── ad_bc_2d.F │ ├── ad_bc_3d.F │ ├── ad_bc_bry2d.F │ ├── ad_bc_bry3d.F │ ├── ad_bulk_flux.F │ ├── ad_congrad.F │ ├── ad_conv_2d.F │ ├── ad_conv_3d.F │ ├── ad_conv_bry2d.F │ ├── ad_conv_bry3d.F │ ├── ad_convolution.F │ ├── ad_def_his.F │ ├── ad_diag.F │ ├── ad_exchange_2d.F │ ├── ad_exchange_3d.F │ ├── ad_extract_obs.F │ ├── ad_force_dual.F │ ├── ad_forcing.F │ ├── ad_frc_adjust.F │ ├── ad_get_data.F │ ├── ad_get_idata.F │ ├── ad_htobs.F │ ├── ad_ini_fields.F │ ├── ad_initial.F │ ├── ad_lmd_swfrac.F │ ├── ad_main2d.F │ ├── ad_main3d.F │ ├── ad_misfit.F │ ├── ad_nesting.F │ ├── ad_obc_adjust.F │ ├── ad_obc_volcons.F │ ├── ad_omega.F │ ├── ad_output.F │ ├── ad_post_initial.F │ ├── ad_pre_step3d.F │ ├── ad_prsgrd.F │ ├── ad_prsgrd31.h │ ├── ad_prsgrd32.h │ ├── ad_prsgrd40.h │ ├── ad_rho_eos.F │ ├── ad_rhs3d.F │ ├── ad_rpcg_lanczos.F │ ├── ad_set_avg.F │ ├── ad_set_data.F │ ├── ad_set_depth.F │ ├── ad_set_massflux.F │ ├── ad_set_vbc.F │ ├── ad_set_zeta.F │ ├── ad_sqlq.F │ ├── ad_step2d.F │ ├── ad_step2d_FB.h │ ├── ad_step2d_FB_LF_AM3.h │ ├── ad_step2d_LF_AM3.h │ ├── ad_step3d_t.F │ ├── ad_step3d_uv.F │ ├── ad_t3dbc_im.F │ ├── ad_t3dmix.F │ ├── ad_t3dmix2_geo.h │ ├── ad_t3dmix2_iso.h │ ├── ad_t3dmix2_s.h │ ├── ad_t3dmix4_geo.h │ ├── ad_t3dmix4_iso.h │ ├── ad_t3dmix4_s.h │ ├── ad_t3drelax.F │ ├── ad_u2dbc_im.F │ ├── ad_u3dbc_im.F │ ├── ad_uv3dmix.F │ ├── ad_uv3dmix2_geo.h │ ├── ad_uv3dmix2_s.h │ ├── ad_uv3dmix4_geo.h │ ├── ad_uv3dmix4_s.h │ ├── ad_uv3drelax.F │ ├── ad_v2dbc_im.F │ ├── ad_v3dbc_im.F │ ├── ad_variability.F │ ├── ad_wrt_his.F │ ├── ad_wvelocity.F │ ├── ad_zetabc.F │ ├── adsen_force.F │ └── adsen_initial.F ├── Bin │ ├── FixDependInfo.pl │ ├── build_roms.csh │ ├── build_roms.sh │ ├── cbuild_roms.csh │ ├── cbuild_roms.sh │ ├── check_nc.csh │ ├── check_nc.sh │ ├── check_openfiles.csh │ ├── check_openfiles.sh │ ├── copyright.csh │ ├── copyright.sh │ ├── cpp_clean │ ├── dates │ ├── dates_test.csh │ ├── dates_test.ksh │ ├── dates_test.sh │ ├── job_afte.csh │ ├── job_afte.sh │ ├── job_array_modes.csh │ ├── job_array_modes.sh │ ├── job_fsv.csh │ ├── job_fsv.sh │ ├── job_fte.csh │ ├── job_fte.sh │ ├── job_i4dvar.csh │ ├── job_i4dvar.sh │ ├── job_i4dvar_sen.csh │ ├── job_i4dvar_sen.sh │ ├── job_normalization.csh │ ├── job_normalization.sh │ ├── job_op.csh │ ├── job_op.sh │ ├── job_r4dvar.csh │ ├── job_r4dvar.sh │ ├── job_r4dvar_sen.csh │ ├── job_r4dvar_sen.sh │ ├── job_rbl4dvar.csh │ ├── job_rbl4dvar.sh │ ├── job_rbl4dvar_sen.csh │ ├── job_rbl4dvar_sen.sh │ ├── job_so_semi.csh │ ├── job_so_semi.sh │ ├── sfmakedepend │ ├── submit_i4dvar.csh │ ├── submit_i4dvar.sh │ ├── submit_mixres_rbl4dvar.sh │ ├── submit_split_i4dvar.sh │ ├── submit_split_r4dvar.sh │ ├── submit_split_rbl4dvar.sh │ ├── substitute │ ├── verify.sh │ ├── ws_remove.csh │ └── ws_remove.sh ├── Drivers │ ├── CMakeLists.txt │ ├── Module.mk │ ├── ad_roms.h │ ├── adsen_roms.h │ ├── afte_roms.h │ ├── array_modes.h │ ├── correlation.h │ ├── fsv_roms.h │ ├── fte_roms.h │ ├── hessian_op_roms.h │ ├── hessian_so_roms.h │ ├── i4dvar.F │ ├── i4dvar_roms.h │ ├── jedi_roms.h │ ├── nl_roms.h │ ├── obs_sen_i4dvar_analysis.h │ ├── obs_sen_r4dvar_analysis.h │ ├── obs_sen_rbl4dvar_analysis.h │ ├── obs_sen_rbl4dvar_forecast.h │ ├── op_roms.h │ ├── optobs_roms.h │ ├── pert_roms.h │ ├── picard_roms.h │ ├── propagator_afte.h │ ├── propagator_fsv.h │ ├── propagator_fte.h │ ├── propagator_hop.h │ ├── propagator_hso.h │ ├── propagator_op.h │ ├── propagator_so.h │ ├── propagator_so_semi.h │ ├── r4dvar.F │ ├── r4dvar_roms.h │ ├── rbl4dvar.F │ ├── rbl4dvar_roms.h │ ├── rp_roms.h │ ├── so_roms.h │ ├── so_semi_roms.h │ ├── split_i4dvar_roms.h │ ├── split_r4dvar_roms.h │ ├── split_rbl4dvar_roms.h │ ├── symmetry.h │ ├── tl_r4dvar_roms.h │ ├── tl_rbl4dvar_roms.h │ ├── tl_roms.h │ └── tlcheck_roms.h ├── External │ ├── behavior_oyster.in │ ├── bio_ECB.in │ ├── bio_Fennel.in │ ├── coupling_inlet_test.in │ ├── coupling_mct.dat │ ├── coupling_test_head.in │ ├── da_roms.tmp │ ├── ecosim.in │ ├── floats_flt_test2d.in │ ├── floats_flt_test3d.in │ ├── floats_lake_signell.in │ ├── floats_upwelling.in │ ├── hypoxia_srm.in │ ├── ice.in │ ├── nemuro.in │ ├── nl_roms.tmp │ ├── npzd_Franks.in │ ├── npzd_Powell.in │ ├── npzd_iron.in │ ├── red_tide.in │ ├── roms_basin.in │ ├── roms_benchmark1.in │ ├── roms_benchmark2.in │ ├── roms_benchmark3.in │ ├── roms_bio_toy.in │ ├── roms_bl_test.in │ ├── roms_canyon2d.in │ ├── roms_canyon3d.in │ ├── roms_channel.in │ ├── roms_damee_4.in │ ├── roms_dogbone_composite.in │ ├── roms_dogbone_refined.in │ ├── roms_dogbone_whole.in │ ├── roms_double_gyre.in │ ├── roms_ducknc.in │ ├── roms_estuary_test.in │ ├── roms_flt_test2d.in │ ├── roms_flt_test3d.in │ ├── roms_grav_adj.in │ ├── roms_inlet_test.in │ ├── roms_kelvin.in │ ├── roms_lab_canyon.in │ ├── roms_lake_jersey.in │ ├── roms_lake_signell.in │ ├── roms_lmd_test.in │ ├── roms_marsh_test.in │ ├── roms_overflow.in │ ├── roms_riverplume1.in │ ├── roms_riverplume2.in │ ├── roms_seamount.in │ ├── roms_sed_test1.in │ ├── roms_sed_toy.in │ ├── roms_shoreface.in │ ├── roms_soliton.in │ ├── roms_test_chan.in │ ├── roms_test_head.in │ ├── roms_upwelling.in │ ├── roms_vegetation_test.in │ ├── roms_wc13.in │ ├── roms_weddell.in │ ├── roms_windbasin.in │ ├── s4dvar.in │ ├── sediment_estuary_test.in │ ├── sediment_inlet_test.in │ ├── sediment_lake_jersey.in │ ├── sediment_lake_signell.in │ ├── sediment_marsh_test.in │ ├── sediment_sed_test1.in │ ├── sediment_sed_toy.in │ ├── sediment_shoreface.in │ ├── sediment_test_chan.in │ ├── sediment_test_head.in │ ├── stations_bl_test.in │ ├── stations_lmd_test.in │ ├── stations_test_head.in │ ├── varinfo.yaml │ ├── vegetation.in │ ├── vegetation_marsh_test.in │ └── vegetation_test.in ├── Functionals │ ├── CMakeLists.txt │ ├── Module.mk │ ├── ana_biology.h │ ├── ana_btflux.h │ ├── ana_cloud.h │ ├── ana_diag.h │ ├── ana_dqdsst.h │ ├── ana_drag.h │ ├── ana_fsobc.h │ ├── ana_grid.h │ ├── ana_hmixcoef.h │ ├── ana_humid.h │ ├── ana_initial.h │ ├── ana_m2clima.h │ ├── ana_m2obc.h │ ├── ana_m3clima.h │ ├── ana_m3obc.h │ ├── ana_mask.h │ ├── ana_nudgcoef.h │ ├── ana_pair.h │ ├── ana_passive.h │ ├── ana_perturb.h │ ├── ana_psource.h │ ├── ana_rain.h │ ├── ana_respiration.h │ ├── ana_scope.h │ ├── ana_sediment.h │ ├── ana_smflux.h │ ├── ana_specir.h │ ├── ana_spinning.h │ ├── ana_sponge.h │ ├── ana_srflux.h │ ├── ana_ssh.h │ ├── ana_sss.h │ ├── ana_sst.h │ ├── ana_stflux.h │ ├── ana_tair.h │ ├── ana_tclima.h │ ├── ana_tobc.h │ ├── ana_vegetation.h │ ├── ana_vmix.h │ ├── ana_winds.h │ ├── ana_wtype.h │ ├── ana_wwave.h │ └── analytical.F ├── Include │ ├── basin.h │ ├── benchmark.h │ ├── bio_toy.h │ ├── bl_test.h │ ├── canyon.h │ ├── channel.h │ ├── channel_neck.h │ ├── coupling_test.h │ ├── cppdefs.h │ ├── damee_4.h │ ├── dogbone.h │ ├── double_gyre.h │ ├── estuary_test.h │ ├── flt_test.h │ ├── globaldefs.h │ ├── grav_adj.h │ ├── inlet_test.h │ ├── kelvin.h │ ├── lab_canyon.h │ ├── lake_jersey.h │ ├── lake_signell.h │ ├── lmd_test.h │ ├── mixed_layer.h │ ├── overflow.h │ ├── riverplume1.h │ ├── riverplume2.h │ ├── seamount.h │ ├── sed_test1.h │ ├── sed_toy.h │ ├── set_bounds.h │ ├── set_bounds_xtr.h │ ├── shoreface.h │ ├── soliton.h │ ├── test_chan.h │ ├── test_head.h │ ├── tile.h │ ├── upwelling.h │ ├── wc13.h │ ├── weddell.h │ └── windbasin.h ├── Modules │ ├── CMakeLists.txt │ ├── Module.mk │ ├── mod_arrays.F │ ├── mod_average.F │ ├── mod_bbl.F │ ├── mod_behavior.F │ ├── mod_biology.F │ ├── mod_boundary.F │ ├── mod_clima.F │ ├── mod_coupler.F │ ├── mod_coupling.F │ ├── mod_diags.F │ ├── mod_eclight.F │ ├── mod_eoscoef.F │ ├── mod_extract.F │ ├── mod_floats.F │ ├── mod_forces.F │ ├── mod_fourdvar.F │ ├── mod_grid.F │ ├── mod_ice.F │ ├── mod_iounits.F │ ├── mod_kinds.F │ ├── mod_mixing.F │ ├── mod_ncparam.F │ ├── mod_nesting.F │ ├── mod_netcdf.F │ ├── mod_ocean.F │ ├── mod_parallel.F │ ├── mod_param.F │ ├── mod_pio_netcdf.F │ ├── mod_scalars.F │ ├── mod_sedbed.F │ ├── mod_sedflocs.F │ ├── mod_sediment.F │ ├── mod_sources.F │ ├── mod_stepping.F │ ├── mod_storage.F │ ├── mod_strings.F │ ├── mod_tides.F │ └── mod_vegetation.F ├── Nonlinear │ ├── BBL │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── bbl.F │ │ ├── bbl_output.F │ │ ├── mb_bbl.h │ │ ├── sg_bbl.h │ │ └── ssw_bbl.h │ ├── Biology │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── biology.F │ │ ├── biology_floats.F │ │ ├── ecb.h │ │ ├── ecb_def.h │ │ ├── ecb_def_pio.h │ │ ├── ecb_inp.h │ │ ├── ecb_mod.h │ │ ├── ecb_var.h │ │ ├── ecb_wrt.h │ │ ├── ecb_wrt_pio.h │ │ ├── ecosim.h │ │ ├── ecosim_def.h │ │ ├── ecosim_def_pio.h │ │ ├── ecosim_inp.h │ │ ├── ecosim_mod.h │ │ ├── ecosim_var.h │ │ ├── ecosim_wrt.h │ │ ├── ecosim_wrt_pio.h │ │ ├── fennel.h │ │ ├── fennel_def.h │ │ ├── fennel_def_pio.h │ │ ├── fennel_inp.h │ │ ├── fennel_mod.h │ │ ├── fennel_var.h │ │ ├── fennel_wrt.h │ │ ├── fennel_wrt_pio.h │ │ ├── hypoxia_srm.h │ │ ├── hypoxia_srm_def.h │ │ ├── hypoxia_srm_def_pio.h │ │ ├── hypoxia_srm_inp.h │ │ ├── hypoxia_srm_mod.h │ │ ├── hypoxia_srm_var.h │ │ ├── hypoxia_srm_wrt.h │ │ ├── hypoxia_srm_wrt_pio.h │ │ ├── nemuro.h │ │ ├── nemuro_def.h │ │ ├── nemuro_def_pio.h │ │ ├── nemuro_inp.h │ │ ├── nemuro_mod.h │ │ ├── nemuro_var.h │ │ ├── nemuro_wrt.h │ │ ├── nemuro_wrt_pio.h │ │ ├── npzd_Franks.h │ │ ├── npzd_Franks_def.h │ │ ├── npzd_Franks_def_pio.h │ │ ├── npzd_Franks_inp.h │ │ ├── npzd_Franks_mod.h │ │ ├── npzd_Franks_var.h │ │ ├── npzd_Franks_wrt.h │ │ ├── npzd_Franks_wrt_pio.h │ │ ├── npzd_Powell.h │ │ ├── npzd_Powell_def.h │ │ ├── npzd_Powell_def_pio.h │ │ ├── npzd_Powell_inp.h │ │ ├── npzd_Powell_mod.h │ │ ├── npzd_Powell_var.h │ │ ├── npzd_Powell_wrt.h │ │ ├── npzd_Powell_wrt_pio.h │ │ ├── npzd_iron.h │ │ ├── npzd_iron_def.h │ │ ├── npzd_iron_def_pio.h │ │ ├── npzd_iron_inp.h │ │ ├── npzd_iron_mod.h │ │ ├── npzd_iron_var.h │ │ ├── npzd_iron_wrt.h │ │ ├── npzd_iron_wrt_pio.h │ │ ├── oyster_floats.h │ │ ├── oyster_floats_def.h │ │ ├── oyster_floats_def_pio.h │ │ ├── oyster_floats_inp.h │ │ ├── oyster_floats_mod.h │ │ ├── oyster_floats_wrt.h │ │ ├── oyster_floats_wrt_pio.h │ │ ├── red_tide.h │ │ ├── red_tide_def.h │ │ ├── red_tide_def_pio.h │ │ ├── red_tide_inp.h │ │ ├── red_tide_mod.h │ │ ├── red_tide_var.h │ │ ├── red_tide_wrt.h │ │ └── red_tide_wrt_pio.h │ ├── CMakeLists.txt │ ├── Module.mk │ ├── SeaIce │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── ice_advect.F │ │ ├── ice_albedo.F │ │ ├── ice_bc2d.F │ │ ├── ice_elastic.F │ │ ├── ice_enthalpy.F │ │ ├── ice_evp.F │ │ ├── ice_evp_sig.F │ │ ├── ice_frazil.F │ │ ├── ice_inp.h │ │ ├── ice_limit.F │ │ ├── ice_mk.h │ │ ├── ice_mod.h │ │ ├── ice_output.F │ │ ├── ice_set_avg.F │ │ ├── ice_smolar.h │ │ ├── ice_spdiw.F │ │ ├── ice_thermo.F │ │ ├── ice_tibc.F │ │ ├── ice_uibc.F │ │ ├── ice_var.h │ │ ├── ice_vbc.F │ │ ├── ice_vibc.F │ │ └── seaice.F │ ├── Sediment │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── mod_vandera_funcs.F │ │ ├── sed_bed.F │ │ ├── sed_bed2.F │ │ ├── sed_bed_cohesive.F │ │ ├── sed_bedload.F │ │ ├── sed_bedload_vandera.F │ │ ├── sed_biodiff.F │ │ ├── sed_flocs.F │ │ ├── sed_fluxes.F │ │ ├── sed_settling.F │ │ ├── sed_surface.F │ │ ├── sedbed_mod.h │ │ ├── sedflocs_mod.h │ │ ├── sediment.F │ │ ├── sediment_def.h │ │ ├── sediment_def_pio.h │ │ ├── sediment_inp.h │ │ ├── sediment_mod.h │ │ ├── sediment_output.F │ │ ├── sediment_var.h │ │ ├── sediment_wrt.h │ │ ├── sediment_wrt_pio.h │ │ ├── sedtr_decay.F │ │ ├── sedtr_reactions_pom.F │ │ └── sedtr_reactions_sed_decay.F │ ├── Vegetation │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── marsh_dynamics.F │ │ ├── marsh_sed_erosion.F │ │ ├── marsh_tidal_range.F │ │ ├── marsh_vert_growth.F │ │ ├── marsh_wave_thrust.F │ │ ├── vegetation_biomass.F │ │ ├── vegetation_drag.F │ │ ├── vegetation_inp.h │ │ ├── vegetation_mod.h │ │ ├── vegetation_output.F │ │ ├── vegetation_stream.F │ │ ├── vegetation_turb.F │ │ └── vegetation_var.h │ ├── WEC │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── wec_dissip.F │ │ ├── wec_output.F │ │ ├── wec_roller.F │ │ ├── wec_stokes.F │ │ ├── wec_streaming.F │ │ ├── wec_u2dbc_im.F │ │ ├── wec_u3dbc_im.F │ │ ├── wec_v2dbc_im.F │ │ ├── wec_v3dbc_im.F │ │ ├── wec_vf.F │ │ ├── wec_wave_mix.F │ │ └── wec_wvelocity.F │ ├── bc_2d.F │ ├── bc_3d.F │ ├── bc_4d.F │ ├── bc_bry2d.F │ ├── bc_bry3d.F │ ├── bulk_flux.F │ ├── bvf_mix.F │ ├── conv_2d.F │ ├── conv_3d.F │ ├── conv_bry2d.F │ ├── conv_bry3d.F │ ├── diag.F │ ├── exchange_2d.F │ ├── exchange_2d_xtr.F │ ├── exchange_3d.F │ ├── exchange_3d_xtr.F │ ├── exchange_4d.F │ ├── forcing.F │ ├── frc_adjust.F │ ├── get_data.F │ ├── get_idata.F │ ├── gls_corstep.F │ ├── gls_prestep.F │ ├── hmixing.F │ ├── ini_fields.F │ ├── initial.F │ ├── interp_floats.F │ ├── lmd_bkpp.F │ ├── lmd_skpp.F │ ├── lmd_swfrac.F │ ├── lmd_vmix.F │ ├── main2d.F │ ├── main3d.F │ ├── mpdata_adiff.F │ ├── my25_corstep.F │ ├── my25_prestep.F │ ├── nesting.F │ ├── obc_adjust.F │ ├── obc_volcons.F │ ├── omega.F │ ├── output.F │ ├── post_initial.F │ ├── pre_step3d.F │ ├── prsgrd.F │ ├── prsgrd31.h │ ├── prsgrd32.h │ ├── prsgrd40.h │ ├── prsgrd42.h │ ├── prsgrd44.h │ ├── rho_eos.F │ ├── rhs3d.F │ ├── set_avg.F │ ├── set_data.F │ ├── set_depth.F │ ├── set_massflux.F │ ├── set_tides.F │ ├── set_vbc.F │ ├── set_zeta.F │ ├── step2d.F │ ├── step2d_FB.h │ ├── step2d_FB_LF_AM3.h │ ├── step2d_LF_AM3.h │ ├── step3d_t.F │ ├── step3d_uv.F │ ├── step_floats.F │ ├── t3dbc_im.F │ ├── t3dmix.F │ ├── t3dmix2_geo.h │ ├── t3dmix2_iso.h │ ├── t3dmix2_s.h │ ├── t3dmix4_geo.h │ ├── t3dmix4_iso.h │ ├── t3dmix4_s.h │ ├── tkebc_im.F │ ├── u2dbc_im.F │ ├── u3dbc_im.F │ ├── uv3dmix.F │ ├── uv3dmix2_geo.h │ ├── uv3dmix2_s.h │ ├── uv3dmix4_geo.h │ ├── uv3dmix4_s.h │ ├── v2dbc_im.F │ ├── v3dbc_im.F │ ├── vwalk_floats.F │ ├── wetdry.F │ ├── wvelocity.F │ └── zetabc.F ├── Obsolete │ ├── hsimt_tvd.F │ ├── t3dbc_ex.F │ ├── tkebc_ex.F │ ├── u2dbc_ex.F │ ├── u3dbc_ex.F │ ├── v2dbc_ex.F │ └── v3dbc_ex.F ├── Programs │ ├── CMakeLists.txt │ ├── Module.mk │ ├── Readme.md │ ├── types.F │ └── yaml_parser_test.F ├── Representer │ ├── Biology │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── rp_biology.F │ │ ├── rp_npzd_Franks.h │ │ ├── rp_npzd_Powell.h │ │ └── rp_npzd_iron.h │ ├── CMakeLists.txt │ ├── Module.mk │ ├── rp_bulk_flux.F │ ├── rp_def_ini.F │ ├── rp_diag.F │ ├── rp_frc_adjust.F │ ├── rp_get_data.F │ ├── rp_get_idata.F │ ├── rp_ini_fields.F │ ├── rp_initial.F │ ├── rp_lmd_swfrac.F │ ├── rp_main2d.F │ ├── rp_main3d.F │ ├── rp_obc_adjust.F │ ├── rp_obc_volcons.F │ ├── rp_omega.F │ ├── rp_output.F │ ├── rp_post_initial.F │ ├── rp_pre_step3d.F │ ├── rp_prsgrd.F │ ├── rp_prsgrd31.h │ ├── rp_prsgrd32.h │ ├── rp_prsgrd40.h │ ├── rp_rho_eos.F │ ├── rp_rhs3d.F │ ├── rp_set_data.F │ ├── rp_set_depth.F │ ├── rp_set_massflux.F │ ├── rp_set_vbc.F │ ├── rp_set_zeta.F │ ├── rp_step2d.F │ ├── rp_step2d_FB.h │ ├── rp_step2d_FB_LF_AM3.h │ ├── rp_step2d_LF_AM3.h │ ├── rp_step3d_t.F │ ├── rp_step3d_uv.F │ ├── rp_t3dbc_im.F │ ├── rp_t3dmix.F │ ├── rp_t3dmix2_geo.h │ ├── rp_t3dmix2_iso.h │ ├── rp_t3dmix2_s.h │ ├── rp_t3dmix4_geo.h │ ├── rp_t3dmix4_iso.h │ ├── rp_t3dmix4_s.h │ ├── rp_t3drelax.F │ ├── rp_u2dbc_im.F │ ├── rp_u3dbc_im.F │ ├── rp_uv3dmix.F │ ├── rp_uv3dmix2_geo.h │ ├── rp_uv3dmix2_s.h │ ├── rp_uv3dmix4_geo.h │ ├── rp_uv3dmix4_s.h │ ├── rp_uv3drelax.F │ ├── rp_v2dbc_im.F │ ├── rp_v3dbc_im.F │ ├── rp_wrt_ini.F │ └── rp_zetabc.F ├── Tangent │ ├── Biology │ │ ├── CMakeLists.txt │ │ ├── Module.mk │ │ ├── tl_biology.F │ │ ├── tl_npzd_Franks.h │ │ ├── tl_npzd_Powell.h │ │ └── tl_npzd_iron.h │ ├── CMakeLists.txt │ ├── Module.mk │ ├── tl_balance.F │ ├── tl_bulk_flux.F │ ├── tl_congrad.F │ ├── tl_conv_2d.F │ ├── tl_conv_3d.F │ ├── tl_conv_bry2d.F │ ├── tl_conv_bry3d.F │ ├── tl_convolution.F │ ├── tl_def_his.F │ ├── tl_def_ini.F │ ├── tl_diag.F │ ├── tl_forcing.F │ ├── tl_frc_adjust.F │ ├── tl_get_data.F │ ├── tl_get_idata.F │ ├── tl_ini_fields.F │ ├── tl_initial.F │ ├── tl_lmd_swfrac.F │ ├── tl_main2d.F │ ├── tl_main3d.F │ ├── tl_nesting.F │ ├── tl_obc_adjust.F │ ├── tl_obc_volcons.F │ ├── tl_omega.F │ ├── tl_output.F │ ├── tl_post_initial.F │ ├── tl_pre_step3d.F │ ├── tl_prsgrd.F │ ├── tl_prsgrd31.h │ ├── tl_prsgrd32.h │ ├── tl_prsgrd40.h │ ├── tl_rho_eos.F │ ├── tl_rhs3d.F │ ├── tl_rpcg_lanczos.F │ ├── tl_set_avg.F │ ├── tl_set_data.F │ ├── tl_set_depth.F │ ├── tl_set_massflux.F │ ├── tl_set_vbc.F │ ├── tl_set_zeta.F │ ├── tl_sqlq.F │ ├── tl_step2d.F │ ├── tl_step2d_FB.h │ ├── tl_step2d_FB_LF_AM3.h │ ├── tl_step2d_LF_AM3.h │ ├── tl_step3d_t.F │ ├── tl_step3d_uv.F │ ├── tl_t3dbc_im.F │ ├── tl_t3dmix.F │ ├── tl_t3dmix2_geo.h │ ├── tl_t3dmix2_iso.h │ ├── tl_t3dmix2_s.h │ ├── tl_t3dmix4_geo.h │ ├── tl_t3dmix4_iso.h │ ├── tl_t3dmix4_s.h │ ├── tl_t3drelax.F │ ├── tl_u2dbc_im.F │ ├── tl_u3dbc_im.F │ ├── tl_uv3dmix.F │ ├── tl_uv3dmix2_geo.h │ ├── tl_uv3dmix2_s.h │ ├── tl_uv3dmix4_geo.h │ ├── tl_uv3dmix4_s.h │ ├── tl_uv3drelax.F │ ├── tl_v2dbc_im.F │ ├── tl_v3dbc_im.F │ ├── tl_variability.F │ ├── tl_wrt_his.F │ ├── tl_wrt_ini.F │ └── tl_zetabc.F ├── Utility │ ├── ADfromTL.F │ ├── CMakeLists.txt │ ├── Module.mk │ ├── array_modes.F │ ├── back_cost.F │ ├── background_std.F │ ├── cgradient.F │ ├── check_multifile.F │ ├── checkadj.F │ ├── checkdefs.F │ ├── checkerror.F │ ├── checkvars.F │ ├── close_io.F │ ├── comp_Jb0.F │ ├── congrad.F │ ├── convolve.F │ ├── cost_grad.F │ ├── dateclock.F │ ├── def_avg.F │ ├── def_dai.F │ ├── def_diags.F │ ├── def_dim.F │ ├── def_error.F │ ├── def_extract.F │ ├── def_floats.F │ ├── def_gst.F │ ├── def_hessian.F │ ├── def_his.F │ ├── def_impulse.F │ ├── def_info.F │ ├── def_ini.F │ ├── def_lanczos.F │ ├── def_mod.F │ ├── def_norm.F │ ├── def_quick.F │ ├── def_rst.F │ ├── def_state.F │ ├── def_station.F │ ├── def_std.F │ ├── def_tides.F │ ├── def_var.F │ ├── destroy.F │ ├── distribute.F │ ├── dotproduct.F │ ├── edit_multifile.F │ ├── equilibrium_tide.F │ ├── erf.F │ ├── extract_field.F │ ├── extract_obs.F │ ├── extract_slice.F │ ├── extract_sta.F │ ├── frc_iau.F │ ├── frc_weak.F │ ├── gasdev.F │ ├── get_2dfld.F │ ├── get_2dfldr.F │ ├── get_3dfld.F │ ├── get_3dfldr.F │ ├── get_bounds.F │ ├── get_cycle.F │ ├── get_env.F │ ├── get_extract.F │ ├── get_grid.F │ ├── get_gst.F │ ├── get_hash.F │ ├── get_metadata.F │ ├── get_ngfld.F │ ├── get_ngfldr.F │ ├── get_nudgcoef.F │ ├── get_state.F │ ├── get_varcoords.F │ ├── get_wetdry.F │ ├── grid_coords.F │ ├── ini_adjust.F │ ├── ini_hmixcoef.F │ ├── ini_lanczos.F │ ├── inner2state.F │ ├── inp_decode.F │ ├── inp_par.F │ ├── inquiry.F │ ├── interpolate.F │ ├── lanc_resid.F │ ├── lapack_mod.F │ ├── lbc.F │ ├── lubksb.F │ ├── ludcmp.F │ ├── memory.F │ ├── metrics.F │ ├── mp_exchange.F │ ├── mp_routines.F │ ├── nf_fread2d.F │ ├── nf_fread2d_bry.F │ ├── nf_fread2d_xtr.F │ ├── nf_fread3d.F │ ├── nf_fread3d_bry.F │ ├── nf_fread3d_xtr.F │ ├── nf_fread4d.F │ ├── nf_fwrite2d.F │ ├── nf_fwrite2d_bry.F │ ├── nf_fwrite3d.F │ ├── nf_fwrite3d_bry.F │ ├── nf_fwrite4d.F │ ├── normalization.F │ ├── nrutil.F │ ├── ntimestep.F │ ├── obs_cost.F │ ├── obs_depth.F │ ├── obs_initial.F │ ├── obs_k2z.F │ ├── obs_read.F │ ├── obs_write.F │ ├── pack_field.F │ ├── packing.F │ ├── posterior.F │ ├── posterior_var.F │ ├── ran1.F │ ├── ran_state.F │ ├── random_ic.F │ ├── read_asspar.F │ ├── read_biopar.F │ ├── read_couplepar.F │ ├── read_fltbiopar.F │ ├── read_fltpar.F │ ├── read_icepar.F │ ├── read_phypar.F │ ├── read_sedpar.F │ ├── read_stapar.F │ ├── read_vegpar.F │ ├── regrid.F │ ├── rep_matrix.F │ ├── roms_interp.F │ ├── round.F │ ├── rpcg_lanczos.F │ ├── set_2dfld.F │ ├── set_2dfldr.F │ ├── set_3dfld.F │ ├── set_3dfldr.F │ ├── set_contact.F │ ├── set_diags.F │ ├── set_grid.F │ ├── set_masks.F │ ├── set_ngfld.F │ ├── set_ngfldr.F │ ├── set_pio.F │ ├── set_scoord.F │ ├── set_weights.F │ ├── shapiro.F │ ├── sqlq.F │ ├── state_addition.F │ ├── state_assign.F │ ├── state_copy.F │ ├── state_dotprod.F │ ├── state_initialize.F │ ├── state_join.F │ ├── state_product.F │ ├── state_read.F │ ├── state_regrid.F │ ├── state_scale.F │ ├── stats.F │ ├── stats_modobs.F │ ├── stdinp_mod.F │ ├── stdout_mod.F │ ├── stiffness.F │ ├── strings.F │ ├── sum_grad.F │ ├── sum_imp.F │ ├── tadv.F │ ├── tides_date.F │ ├── tile_indices.F │ ├── time_corr.F │ ├── timers.F │ ├── uv_rotate.F │ ├── uv_var_change.F │ ├── vorticity.F │ ├── white_noise.F │ ├── wpoints.F │ ├── wrt_aug_imp.F │ ├── wrt_avg.F │ ├── wrt_dai.F │ ├── wrt_diags.F │ ├── wrt_error.F │ ├── wrt_evolved.F │ ├── wrt_extract.F │ ├── wrt_floats.F │ ├── wrt_gst.F │ ├── wrt_hessian.F │ ├── wrt_his.F │ ├── wrt_impulse.F │ ├── wrt_info.F │ ├── wrt_ini.F │ ├── wrt_quick.F │ ├── wrt_rst.F │ ├── wrt_state.F │ ├── wrt_station.F │ ├── wrt_std.F │ ├── wrt_tides.F │ ├── yaml_parser.F │ └── zeta_balance.F └── memory.txt ├── User ├── External │ ├── behavior_oyster.in │ ├── bio_ECB.in │ ├── bio_Fennel.in │ ├── coupling.in │ ├── ecosim.in │ ├── floats.in │ ├── floats_adria02.in │ ├── hypoxia_srm.in │ ├── nemuro.in │ ├── npzd_Franks.in │ ├── npzd_Powell.in │ ├── npzd_iron.in │ ├── red_tide.in │ ├── roms.in │ ├── roms_adria02.in │ ├── roms_cblast.in │ ├── roms_doppio.in │ ├── roms_eac_4.in │ ├── roms_eac_8.in │ ├── roms_ias.in │ ├── roms_ias_40.in │ ├── roms_natl.in │ ├── roms_nena.in │ ├── roms_nj_bight.in │ ├── roms_scb.in │ ├── roms_sw06_coarse.in │ ├── roms_sw06_fine.in │ ├── roms_wcofs.in │ ├── s4dvar.in │ ├── sediment.in │ ├── sediment_adria02.in │ ├── stations.in │ └── stations_adria02.in ├── Functionals │ ├── ana_biology.h │ ├── ana_btflux.h │ ├── ana_cloud.h │ ├── ana_diag.h │ ├── ana_dqdsst.h │ ├── ana_drag.h │ ├── ana_fsobc.h │ ├── ana_grid.h │ ├── ana_hmixcoef.h │ ├── ana_humid.h │ ├── ana_initial.h │ ├── ana_m2clima.h │ ├── ana_m2obc.h │ ├── ana_m3clima.h │ ├── ana_m3obc.h │ ├── ana_mask.h │ ├── ana_nudgcoef.h │ ├── ana_pair.h │ ├── ana_passive.h │ ├── ana_perturb.h │ ├── ana_psource.h │ ├── ana_rain.h │ ├── ana_respiration.h │ ├── ana_scope.h │ ├── ana_sediment.h │ ├── ana_smflux.h │ ├── ana_specir.h │ ├── ana_spinning.h │ ├── ana_sponge.h │ ├── ana_srflux.h │ ├── ana_ssh.h │ ├── ana_sss.h │ ├── ana_sst.h │ ├── ana_stflux.h │ ├── ana_tair.h │ ├── ana_tclima.h │ ├── ana_tobc.h │ ├── ana_vmix.h │ ├── ana_winds.h │ ├── ana_wtype.h │ └── 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