EMS Release v1.5.3

COMPAS v1.4.2

• Re-worked universal limiter
• Added tracer advection sub-step safety factor over-ride
• Fix for Lipschitz condition
• Fix indexing issue for sediment Mesh2_layers and layerfaces and write out tracer attributes in output file

SHOC v1.3.2

• Bugfix on DHD (df_has_time)
• Fix segfault for sigma runs
• Bugfix: prevent reading transport data beyond stop time

EMSLIB v1.4.1

• Inclusion of nanoflan's kdtree (configure with --enable-kdtree
• Significantly improves performance for FFSL tracer advection & particle tracking
• Fix: string_utils Conditional Jump valgrind error

ECOLOGY v1.3.2

• Generate netCDF ecology_parameter_setup.nc file
• Streamlined writing of setup files
• UTC correction for moonvars and removed moon phase calculation

SEDIMENTS v1.1.4

• Fix memory lead in sed2hd

EMS Release v1.5.2

• GCC 12.x compliance
• Bugfix for seg. fault when invoking sigma coordinates
• Re-structure of testing scripts

EMS Release v1.5.1

COMPAS v1.4.1

• Added compatibility for pre-V7367 transport scheduling
• Added spatially variable VZ0, KZ0
• Included elliptical mesh functions

SHOC v1.3.1

• Added compatibility for pre-V7367 transport scheduling

EMSLIB v1.3.1

• gcc 11.x compliant
• Included elliptical mesh functions

ECOLOGY v1.3.1

• various moonvars update

EMS Release v1.5.0

COMPAS v1.4.0

• Nearshore wave interactions via SWAN (Section 4.21.1 User's manual)
• Included reading of multiple tide files (Section 4.11.23 User's Manual)
• Save maximum difference for monotonic violations (Section 4.31.24 User's Manual)
• Added UGRID reading for transport mode. Added reading of layer thickness (Section 9.4 User's Manual)
• Added upper limit for viscosity using optimized crash recovery (Section 6.4 User's Manual)
• Added input of longwave downwelling, specific humidity for heatfluxes (Section 4.18 User's Manual)
• Improved bathy interpolation with chunking, convex hull subsetting, .mnc input (Section 4.9 User's Manual)
• Added ability to read IMOS mooring netCDF formatted files. Added vertical interpolation metric (Sections 4.31.22 & 4.32.5 User's Manual)
• Added region definition using metis (Section 4.31.21 User's Manual)
• Added kinetic energy options (Section 4.12 User's Manual)
• Bugfix in Window map file

SHOC v1.3.0

• Added provision to output UGRID format
• Bugfix in cs_land_fill()
• Bugfix in reading 3D swr attenuation
• Allow longwave components, specific humidity input for BULK heatflux
• Begin ginterface consolidation work

EMSLIB v1.3.0

• Fixed provision to mesh within the closed OBC path (no start/end indices) - coastmesh
• Improved reading CF netCDF without coordinate attributes
• Cascade search on missing and fill values for CF netCDF
• Included nearest_within_eps interpolation to read SIMPLE files
• Bugfix to read new data when a netCDF file is updated
• Semi-lagrange tracing routines on unstructured mesh

ECOLOGY v1.3.0

• Added new column-based light model process (light_spectral_col) that uses mass-specific optical properties specified in the tracer list to calculate inherent optical properties (e.g. total absorption) and apparent optical properties (e.g. downwelling light, remote-sensing reflectance). Outputs optical parameters into optical_setup.nc, and full optical output of individual columns into optical_column_out_X.nc. Light_spectral_col has improved moonlight / starlight calculations.
• Added new age tracer into process mixed_layer_age_col that uses the mixed_layer_depth calculation in hydro model to age water only in the surface mixed layer.
• Added shear stress mortality to existing coral bleaching process.
• Updated zooxanthellae expulsion parameterisation.
• Added new process for growth and mortality of free-living zooxanthellae.
• Changed name for suspended macroalgae to SMA to allow both suspended and benthic macroalgae (and fixed minor bug in growth of SMA).
• Added processes for dimethyl sulphide production and air sea exchange (dimethyl_sulphide_wc).
• Replaced almost all einterface commands with ginterface commands.
• New temperature dependence for Trichodesmium (default is old).
• Added new process diffusion_heat_epi to nudge sediment temperature and salt to bottom water column value.

SEDIMENTS v1.1.3

• Fixed segfault in spatial tracer initialisation

WAVES v2.0.0

• SWAN library interface
• Inclusion of wavenumber and Bernoulli head

EMS Release v1.4.0

COMPAS v1.3.0

• Included flux adjustment scaling options (Section 4.11.9 User's Manual)
• Included LUST/CLUST scheme for momentum advection.
• Added swan conversion routine.
• Added 2nd order FFSL scheme.
• Added split LAPLACIAN/BIHARMONIC momentum mixing.
• Added split tracer advection (FFSL and QUICKEST).
• Improved TILED 2-way nesting (improved barotropic coupling).
• Included automated import of 2D and 3D fields (Section 4.31.24 User's Manual).
• Added history, crash log (Section 4.33 User's Manual)
• Added flux adjustment boundary scaling (Section 4.11.9 User's Manual)
• Added tidal velocity forcing added to CUSTOM forcing (Section 4.11.23 User's Manual)
• Added regionalised tracer initialisation (Section 4.10 User's Manual)
• Added regionalised horizontal mixing (Section 4.23 User's Manual)
• Added test cases setup (Section 12 User's Manual)
• Added cell areas for RESOLUTION (Section 4.31.14 User's Manual)
• Added glider scaling function (Section 4.10.5 User's Manual)
• Added ROAMv5 (Section 7 User's Manual)

SHOC v1.2.0

• Add region specification using polygon specification in .bnc file and poly_contains_point().
• Initialize dhw diagnostic schedule after dumps for daily nrt operation.
• Copy u1/u2 resets to velocity arrays.
• Included automated import of 2D and 3D fields (Section 4.31.24 User's Manual).
• Added ROAMv5 (Section 7 User's Manual)
• Added flux adjustment boundary scaling (Section 4.11.9 User's Manual)
• Allow regionalised 2D interpolation on resets.
• Allow regionalised estimation of swr parameters.
• Added density diagnostic.
• Added equilibrium tide variables.
• Added enhanced tracer interpolation (Section 4.10 User's Manual)
• Added MINMAX neighbourhood metric for time-series (Section 4.32.5 User's Manual).
• Included scaling to glider data (Section 4.10.5 User's Manual).
• Expanded GHRSST swr parameterisation.
• Added additional model descriptors (Section 4.1 User's Manual).
• Added ability to process multiple DHW diagnostics (Section 4.31.15 User's Manual).
• Bugfix for transport volume fluxes.
• Bugfix to GHRSST SWR parameterisation

EMSLIB v1.2.1

• Incorporate model/lib/grid into emslib
• Added ability for unstructured grid interpolation

ECOLOGY v1.2.0

• Added tasse1p0 parameter defaults with keyword "TASSE1p0"
• Added "TASSE1p0" process defaults with keyword "TASSE1p0"
• Added "PORE" process default with keyword "porewater"
• Increased allowable number of optical wavlengths from 25 to 250
• Added options of red, green and brown macroalgae, defaulting to brown.
• Updated check for tracer diag flag so that all warnings in runlog should be taken seriously.
• Updated filter_feeder_epi process for Storm Bay, with parameter reads, outputs to ecology_setup.txt etc.
• Removed calculation in value_common of EpiOxy & EpiNH4.
• Alignment of all units of diagnostic variables with names "_rm", "_pr", "_gr".
• Fixed in bug light_spectral_wc bugged that meant if moonlight calculations were invoked then pigment absorption defaulted to Gaussian.
• Include a large number of new default parameter values in ecological processes.
• Anammox revised with oxygen removed from system. Anammox equation changed to a minimum function. No anammox in sediment layers thicker than 20 cm.
• Check-in Nugzar's changes so that unstructured model works.
• In moon.c, fixed Julian day bug.

SEDIMENTS v1.1.2

• Default minseddz parameter to 1e-6m

Tracerstats v1.0.1

• Bugfix to RMSE

EMS Release v1.3.0

COMPAS v1.2.0

• New FFSL scheme.
• Allow FFSL to be used with mean TRANSPORT.
• Moved mean computations to a scheduled function.
• Included ADJUST_RATIO for OBCs (Section 4.11.9 User's Manual).
• Explicit tide constituents specified via TIDE_CONSTITUENTS_VEL & TIDE_CONSTITUENTS_TRAN (Section 4.11.23 User's Manual).
• Added Courant number (Section 4.31.9 User's Manual), monotonicity diagnostics.
• Added window partitioning using METIS
• Added windows partitioning from regions (Section 4.2 Users's Manual).
• Added HFUN options (POLY & mixed conditions) (Section 14 Users's Manual).
• Added minimum bathymetry defined within a polygon (Section 4.9 Users's Manual).
• Included OBC T/S nudging zones (Section 4.11.12 User's Manual).
• Included surface heatflux relaxation to GHRSST (Section 4.18 User's Manual).
• Added automated cookie cut.
• Include length factors in tangential velocity diagnostic calculation.
• Bugfix on baroclinic pressure calculation.

SHOC v1.1.3

• Included OBC T/S nudging zones (Section 4.11.12 User's Manual).
• Included surface heatflux relaxation to GHRSST (Section 4.18 User's Manual).
• Added DHW computation options.
• Bugfiix in ginterface_calc_zenith to restore the longitude based calculation that got reverted in Feb. 2019
• Included tracer OBC prescribed using tracer in tracer list.
• Include 3D tracer from normalized profile.
• Bugfix for SWR initialisation.
• Do SWR parameter estimation using data at depth.
• Moved mean computations to a scheduled function.

EMSLIB v1.1.0

• Re-org of moon light calculation to support Ecology

ecology v1.2.0

• Add support for moon light calculations in light_spectral
• New processes: p_adsorption.c, nitrification_denitrification_anammox and age_sed

sediments v1.1.1

• Minor changes for default values of css_er_val & css_er_depth in auto tracers

EMS Release v1.2.1

• Fix COMPAS build error
• Fix parameter file paths in model/tests/hd-us

EMS Release v1.2

COMPAS v1.1.3

• Include bathymetry MAXDIFF and median filtering (Section 4.8 User's Manual).
• Allow unstructred interpolation from multiple input files (Section 4.8 User's Manual).
• Included parray and memory output.
• Included momentum tendency arrays (compatibe v6257 uses previous method).
• Improvements to viscosity scaling (using edge area).
• Included cookie cuts.
• Included tidal energy extraction.
• Optimise mask array reset in build_quadratic_weights
• Included equilibrium tidal forcing (Section 4.4 User's Manual).
• Included custom tide diagnostic (Section 4.31.14 User's Manual)
• Included tracer profiles scaled to a surface 2D distribution (Section 4.31.23 User's Manual)
• Included eta relaxation to custom tide (Section 4.13.1 User's Manual).
• Included bathy masking and smoothing within a polygon (Section 4.9 User's Manual).
• Included APVM method for momentum advection (Section 4.12 User's Manual).
• Improved tidal forcing for 2D mode.

EMSLIB

• Enable single level chunking for netCDF4

EMS Release v1.1.1

COMPAS v1.1.2

• Fix "Run start" header
• Fix build error

EMS Release v1.1

Updates to the following modules:

COMPAS v1.1.1

• Added diagnostic for cell centered viscosity (Section 4.31.14 User's Manual).
• Added stereographic and power meshes (Section 4.7.5 User's Manual).
• Added land ommision (NLAND, Section 4.9 User's Manual).
• Added Manning bottom friction for 2D mode (Section 4.20 User's Manual).
• Added reading of sediment variables.
• Added dedicated monotone least squares linear interpolation for FFSL transport.
• Included normalized vertical profiles
• Included Simpson-Hunter tidal front diagnostic
• Included glider time series diagnostic
• Included biharmonic momentum mixing
• Included alternative potential vorticity momentum formulations
• Included POINT weighting functions
• Included explicit override capability for bathy weighting functions
• Allow means to operate on auto tracers
• Various bug fixes

SHOC v1.1.1

• MEAN counters in the restart file
• Added normalized vertical profile diagnostic (Section 3.31.23 User's Manual).
• Added mean tracer (including auto tracers) (Section 3.31.2 User's Manual).
• Various bug fixes

gridlib v1.1.0

• Added linear least squares interpolation function

waves v1.0.1

• Initial ginterface changes

sediments v1.1.0

• O2 sediment/water flux diagnostics

ecology v1.1.1

• New dinoflagellate spectral mortality water column process
• includes various bug fixes

This is the version of the ecology code that was used in SIMA Austral phase 1 and the eReefs GBR4_H2p0_B3p0 model

model/tests/hd-us

• Updates to closed, test2 and cetas COMPAS tests