Here is a list of all files with brief descriptions:

[detail level 1234]

docs
► Master
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
ad_biology.F
ad_npzd_Franks.h
ad_npzd_iron.h
ad_npzd_Powell.h
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
► Drivers
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
► 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
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
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_sediment.F
mod_sources.F
mod_stepping.F
mod_storage.F
mod_strings.F
mod_tides.F
► Nonlinear
► BBL
bbl.F
bbl_output.F
mb_bbl.h
sg_bbl.h
ssw_bbl.h
► Biology
biology.F
biology_floats.F
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_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
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
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
► SeaIce
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
sed_bed.F
sed_bedload.F
sed_fluxes.F
sed_settling.F
sed_surface.F
sedbed_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
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_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
types.F
yaml_parser_test.F
► Representer
► Biology
rp_biology.F
rp_npzd_Franks.h
rp_npzd_iron.h
rp_npzd_Powell.h
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
tl_biology.F
tl_npzd_Franks.h
tl_npzd_iron.h
tl_npzd_Powell.h
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
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_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_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
regrid.F
rep_matrix.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_copy.F
state_dotprod.F
state_initialize.F
state_join.F
state_product.F
state_read.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