Release 9.0.0 (02/12/2024)
==========================

TELEMAC-2D: fix time series output when different output times are required
for different output files (in TIME SERIES COORDINATES FILE 1 and 2)

PYTHON: the Fortran compiler is now correctly set when F2PY uses Meson as its
backend.

PYTHON: major improvement of the alter functionnality from run_telfile.py
regarding performance and memory consumption.

COURLIS: fix an error in planma which induces no updates of transcritical
variables (MASCARET kernel) with profiles evolution

TELEMAC-3D/GAIA: fix mass conservation of tracers when bottom evolution
if coupling TELEMAC-3D with GAIA

PYTHON: fix a potential crash when using TelemacFile.set_data_on_polygon with
Python 3.11 due to the removal of the getargspec function from the inspect
module

STBTEL: integer values to describe open boundaries are now correctly taken from
the input file when using tracers

MASCARET: implement VnV check_results and add validation documentation for all
test cases

TELEMAC-2D/TELEMAC-3D/WAQTEL: fix inconsistent units for pressure
New keyword PRESSURE UNIT in TELEMAC-2D and TELEMAC-3D dictionaries
(default = 1 for Pa/SI, other choice 2 for hPa)

TELEMAC-2D: fix shift of time when computing maximum values in RESTART FILE
(e.g. maximum elevation, maximum velocity, maximum water depth)

TELEMAC-3D: new option 5 for TRACERS VERTICAL PROFILES
(user defined profile and imposed concentration) in addition to current option 0
(profile directly defined by user with tracers values)

TELEMAC-2D: wall treatment for mixing length turbulence model

TELEMAC-2D: Coupling WAQTEL with the finite volumes part

TELEMAC-2D: The telemac2d.F subroutine has been duplicated in telemac2d.F
for the finite element resolution methods and telemac2d_fv.F for finite
volumes resolution method.

ARTEMIS: fix when AUTOMATIC TETAP CALCULATION is true. The wave angle at the
boundary is changed to the angle of the incoming wave.

TELEMAC-2D/TELEMAC-3D/TOMAWAC/GAIA: computation now crashes with
time series files if output point outside the domain

TELEMAC-2D: Fix time step adaptation to graphic printouts in finite volumes

PYTHON: fix Geoportail link in pretel function clc.py

TELEMAC-2D: Message error if using variable time step and coupling with TOMAWAC

PYTHON: add support for setuptools version 74.0.0 and later when using F2PY.

PYTHON: remove the dicofile argument from TelApy module constructors and use
telemac_cas.get_dico to retrieve the dictionary for each module.

TELEMAC-3D: fix error message when wrong number of values of tracers at sources
if coupling with GAIA and suspended sediments

TELEMAC-2D/TELEMAC-3D: fix wrong place to call user Fortran for sources
when dealing with flowrates or tracers

TELEMAC-3D: new option for MESH TRANSFORMATION (= 4) for specifying sigma
coordinates with a zooming factor near the bottom and near the free surface

TELEMAC-2D: new variables maximum water depth, maximum flowrate and associated
time for graphic printouts

TELEMAC-2D/GAIA: in parallel, replace multiple calls to P_MIN and P_MAX with
a single call to P_MIN_ARRAY and P_MAX_ARRAY. Also introduce the subroutine
P_SUM_ARRAY with the same interface as P_MIN_ARRAY.

TOMAWAC: add functionality to have different time steps for different processes.
Using this functionality, substantially faster calculation times can be obtained.

TOMAWAC: fix a bug causing a crash when using spectra boundary
conditions, when doing multiple runs with TelApy.

TOMAWAC: added limiter on spectral velocities according to Dietrich et al (2013)

TOMAWAC: optimized qveg, qporos and qdscur, by removing usused variable TSDER and
optimizing some loops.

TOMAWAC: add output for the peak wave direction

TELEMAC-2D: add new section in documentation 'Option 2: Generic weirs'

PYTHON: remove all calls to sys.exit all from Python functions, allowing them
to be called from any module.

PYTHON: executing run_telfile.py without arguments now displays information
about the usage of the script.

PYTHON: complete rewrite of the contour extraction algorithm of the
extract_contour module, resulting in a massive speed-up.

PYTHON: check_cas (from the TelemacCas class) now allows int and float for
float keywords.

PYTHON: optimisation of generate_atm by replacing the use of the old Selafin
class with the TelemacFile class. Also fixed the misnamed parameter "ll2utm" to
"utm2ll".

API: add parameter variables in TOMAWAC API to be able to access to more
parameters in the modeling (breaking dissipation, strong current, wind input)

PYTHON: add F2PY support for Python 3.12 onwards. F2PY uses Meson as its
default backend in this case, which must be installed for proper generation of
of the API and HERMES Python wrappers.

PYTHON: fix a memory leak when calling TelemacFile.interpolate_mesh_on_points
caused by a circular dependency in Matplotlib.LinearTriInterpolator.

TELEMAC-2D: steady state message only written when reached for every subdomain
in parallel

TELEMAC-2D: fix wrong test to compute CSO2 in PRERES_TELEMAC2D
(not done for time series file)

WAQTEL: fix formulae of saturation vapour pressure (Magnus-Tetens equation)
restoring removed brackets

TOMAWAC: Optimisation of reading telemac file: by saving the record of the
last read we do not have to read from the beginning at each time step.

PYTHON: huge performance improvement in the extract_contour function from
pretel.

TELEMAC-2D: fix the filling of MVIST (FV scheme for tracer diffusion) in LECDON

TELEMAC-3D: fix vertical diffusion with hydrostatic inconsistencies filter.
The vertical diffusion must be taken into account in inconsistent elements,
otherwise the bottom friction is not taken into account correctly

PYTHON: use HOMETEL in get_dico from telemac_cas.py when CFGS is not
initialised.

PYTHON: fix HERMES Python extension module generation with older versions of
F2PY, such as 1.19 or 1.20.

TELEMAC-3D: new keyword USE MAXIMUM VALUES FROM PREVIOUS COMPUTATION FILE
to compute maximum values for variables MAXZ and TMXZ from a previous
computation and the current computation or only from the current computation
as done in TELEMAC-2D

TELEMAC-3D: fix chacteristics in spherical coordinates in 3D (UCONVC and VCONVC
have to be updated with COSLAT only with this combo of 2 options)

TELEMAC-3D: fix spherical coordinates in 3D (LONGITU was called twice)

PYTHON: major improvement of the merge functionnality from run_telfile.py
regarding performance and memory consumption.

HERMES: huge speedup when reading and writing large SELAFIN files.

PYTHON: add a new "timeit" decorator to benchmark a Python function using a
performance counter.

TELEMAC-2D: fix the initialisation of work arrays to 0 before calling VECTOR
for a few subroutines

TELEMAC-3D: fix the initialisation of work arrays to 0 before calling VECTOR
for a few subroutines

GRETEL: fix date and time not written in the 3D result file in parallel

GAIA: fix the index of the EBOR%ADR table given as input to the BEDLOAD_EVOL
subroutine in bedload_main.f because this table is filled with NSICLA and not
NSAND.

PYTHON: several fixes to TelemacFile
  - The nplan property now uses the same convention as in Fortran and therefore
  returns 0 for a 2D mesh instead of 1.
  - The ipobo array is now correctly read from a SELAFIN file even if no
  boundary condition file has been given to the constructor.

TELEMAC-2D: new default value for ACCURACY FOR DIFFUSION OF TRACERS = 1.E-8
like in TELEMAC-3D (old default = 1.E-6)

TELEMAC-2D: new default value for SCHEME FOR ADVECTION OF TRACERS = 13 (NERD)
and 3rd component of TYPE OF ADVECTION (for tracers) to have a mass-conservative
advection scheme which works with tidal flats
(old choice = 1 i.e. characteristics)

TELEMAC-2D/TELEMAC-3D: new default value for TREATMENT OF NEGATIVE DEPTHS
= 2 (flux control) to always have positive depths, old default = 1 (smoothing)
Mandatory options to use this choice are now automatically set with a
warning message if using this new default choice

PYTHON: fix the calculation of normals and tangents in polyline_integrals,
which was not carried out properly for each segment.

PYTHON: fix generate_atm.py for v8p5 name conventions

BIEF: MUMPS is no longer limited to versions 4.10 and 5.2.1. The warning
is now only displayed for versions lower than 4.10.

TELEMAC-3D: fix index error to clip rain temperature

TELEMAC-3D: fix if 3 subdomains join at the same node on a solid boundary
in parallel

TELEMAC-2D: Deleted boolean keywords, features activated by files
  - COMPUTATION CONTINUED (when PREVIOUS COMPUTATION FILE)
  - VALIDATION (when REFERENCE FILE)
  - RESTART MODE (when RESTART FILE)
  - OIL SPILL MODEL (when OIL SPILL STEERING FILE)
  - FLUXLINE (when FLUXLINE INPUT FILE)
  - BREACH (when BREACHES DATA FILE)
  - VELOCITY FOR DELWAQ (when VELOCITY DELWAQ FILE)
  - DIFFUSIVITY FOR DELWAQ (when DIFFUSIVITY DELWAQ FILE)
  - TEMPERATURE FOR DELWAQ (when TEMPERATURE DELWAQ FILE)
  - SALINITY FOR DELWAQ (when SALINITY DELWAQ FILE)

TELEMAC-3D: Deleted boolean keywords, features activated by files
  - COMPUTATION CONTINUED (when PREVIOUS COMPUTATION FILE)
  - 2D CONTINUATION (when FILE FOR 2D CONTINUATION)
  - VALIDATION (when REFERENCE FILE)
  - RESTART MODE (when RESTART FILE)
  - OIL SPILL MODEL (when OIL SPILL STEERING FILE)
  - VELOCITY FOR DELWAQ (when VELOCITY DELWAQ FILE)
  - DIFFUSION FOR DELWAQ (when DIFFUSIVITY DELWAQ FILE)
  - TEMPERATURE FOR DELWAQ (when TEMPERATURE DELWAQ FILE)
  - SALINITY FOR DELWAQ (when SALINITY DELWAQ FILE)

GAIA: Deleted boolean keywords, features activated by files
  - COMPUTATION CONTINUED (PREVIOUS SEDIMENTOLOGICAL COMPUTATION FILE)
  - VALIDATION (when REFERENCE FILE)
  - RESTART MODE (when RESTART FILE)
  - FLUXLINE (when FLUXLINE INPUT FILE)

WAQTEL/KHIONE: Deleted keyword:
  - VALIDATION

TELEMAC-3D: new default vertical turbulence model: Nezu & Nakagawa model
(mixing length) rather than old constant viscosity
and default mixing length model is Nezu & Nagawa = 3 (old = Prandtl = 1)

TELEMAC-2D/TELEMAC-3D: same default values for 2 keywords
LATITUDE OF ORIGIN POINT and SPATIAL PROJECTION TYPE in 2D and 3D

TELEMAC-3D: change the dimension of keyword SUPG OPTION
1 single integer replaces the previous 4 integer array (default = 1)
as only the 1st component was used

TOMAWAC: Provide a unique file to read water depth AND current.
This unique file is the one defined by CURRENT FILE keyword.

TOMAWAC: Correct the water depth at the initialisation of a hotstart in
case TELEMAC-2D would provide a water depth null in its file.

TELEMAC-2D: fix use of work arrays in preres_telemac2d to store celerity and
free surface rather than FU and FV as preres_telemac2d is called early in the
time loop when coupling with GAIA

TELEMAC-3D: wrong tests when coupling with GAIA with a 3rd module

TELEMAC-2D FV / GAIA: fix erosion and deposition source terms

TELEMAC-2D: fix initialization of YASMO variable in prosou

KHIONE: Adding Bulk formula to better represent thermal exchanges between
oceanic water and air.

Release V8P5R0 (01/12/2023)
===========================

COURLIS: fix wrong integration of historical numerical scheme for bedload from
now named adaptative scheme, add a new one "Finite Volume Upwind scheme" and a
new option to define control cells of the scheme chosen (colocated with
hydraulic or staggered).
New keywords for COURLIS:
 - SCHEMA NUMERIQUE POUR LE CHARRIAGE to choose the numerical scheme for
bedload
 - DEFINITION DES VOLUMES DE CONTROLE POUR LE CHARRIAGE to choose the
definition of control cells

WAQTEL: fix reaeration + degassing enabled for O2 in 2D

WAQTEL: fix wrong implementation of 3D equations in EUTRO, BIOMASS and O2:
- benthic flux applied at the bottom layer (EUTRO+O2)
- reaeration + degassing enabled (EUTRO+O2)
- unit consistency (EUTRO+O2)
- temporary disabling of sedimentation velocities for N, P (EUTRO+BIOMASS)
+ Organic Load (EUTRO)

WAQTEL: fix wrong implementation of 3D equations in MICROPOL

GAIA: Add a new test case to check the cohesive erosion and deposition
fluxes with an analytical solution

BIEF: fix the overflow of paraco message tags

PYTHON: fix the generation of the API and Hermes Python wrappers when using the
latest versions of F2PY (1.24.x and above).

PYTHON: New option for compile_telemac.py --check that checks the coding
convention (replacing check_code.sh)

PYTHON: Correctiong telemac_file.get_horizontal_slices was not working with
float + issue in code

KHIONE: Kills wrong thermal term from ice cover to water

TELAPY: Correcting issue for mpi_get when on interface point

PYTHON: If a rotation is asked with run_telfile.py alter the velocity is rotated

KHIONE: seeding deactivated when water temperature is higher than 0

TELEMAC-2D/WAQTEL: fix call to METEO at initial time step when coupling
TELEMAC-2D with WAQTEL

STBTEL: fix a long-standing regression that prevented dry elements from being
suppressed since V7P0

TELEMAC-2D/TELEMAC-3D: new keyword INITIAL TIME (default = 0.)
to enable to change it outside CONDIN and CONDIM subroutines

TOMAWAC : There mustn't be bottom friction for infinite depth.

WAQTEL: fix computation of air density in thermal exchange formula in 3D
(exchange_with_atmosphere.f)

TELEMAC-3D: fix tracers not initialised correctly if continuing a 2D computation

TELEMAC-3D: fix the loss of accuracy when continuing computation with
k-epsilon or k-omega turbulence model + hydrostatic version

TELEMAC-3D: fix the loss of accuracy when continuing computation with
k-omega turbulence model

Python: fix errors with latest versions of NumPy and Matplotlib

TELEMAC-3D: fix the loss of accuracy when continuing computation with
Spalart-Allmaras turbulence model

TOMAWAC: add surface rollers energy balance
New keywords:
 - SURFACE ROLLERS
 - NUMBER OF SURFACE ROLLER TIME STEPS
 - BETA S SURFACE ROLLERS
 - BETA 2 SURFACE ROLLERS

TELEMAC-2D/TELEMAC-3D: new keyword ATMOSPHERIC PRESSURE AT TIDAL BOUNDARIES
(Inverted barometer effect)

GAIA: remove "_GAIA" suffixes from most subroutines and functions, especially
those originally imported from SISYPHE.

TELEMAC-2D/TELEMAC-3D: soft boundaries to prevent unrealistic jetting flows
at open boundaries

TELEMAC-3D/TOMAWAC: faster three-dimensional coupling between TELEMAC and TOMAWAC
(30% speed up of Rip test case)

MASCARET: New option for storing results

COURLIS: Add a new option for bottom evolution with uniform erosion and uniform
deposition with:
 - New keywords:
   - to activate it: OPTION FOR PROFILE EVOLUTION = 2 (historic
option is 1 and is kept by default)
   - to define width of erosion on the cross-section by imposing an "elevation
for erosion":
     IMPOSED ELEVATION FOR EROSION or FILE FOR IMPOSED ELEVATIONS FOR EROSION
 - specific "planimetrage" functions have been developped for this option in
order to optimize calculation time
 - Documentation and VnV with 2 test-cases

TELEMAC-2D/TELEMAC-3D: time optimisation when using BINARY ATMOSPHERIC DATA FILE
provided that it follows the format expected by METEO_TELEMAC module

TELEMAC-3D: control sections in 3D from bottom to free surface
using depth averaged velocity components

TELEMAC-2D/TELEMAC-3D/TOMAWAC/GAIA: time series files to save results
at selected points and periods of time with different frequencies
from classical graphic printout period

COURLIS: for suspension transport, new option for effective shear stress
formula (with or without approximation H ~ Rh).

BIEF: fix shift index when reading BINARY ATMOSPHERIC DATA FILE and using
GET_DATA_VALUE subroutine from METEO_TELEMAC module

WAQTEL: new law to compute oxygen saturation concentration (Benson and Krause)
depending on water temperature and salinity

WAQTEL: new variables oxygen saturation concentration (CSO2) and percentage
of oxygen saturation (O2SAT) in result files (TELEMAC-2D and TELEMAC-3D)

GAIA: original date and hour of time now come from TELEMAC.
Deleted GAIA keywords:
- ORIGINAL DATE OF TIME
- ORIGINAL HOUR OF TIME

Python: Add a pretel script to construct the spectrum on the boundary
of a domain for a TOMAWAC calculation

COURLIS: add 3 new test-cases and complete VnV with epsilons and a new VnV
documentation

TELEMAC-2D/TELEMAC-3D: new harmonic constants database HAMTIDE model available
to compute tidal boundary conditions and initial conditions
New keyword: VELOCITIES IN BINARY DATABASE 2 FOR TIDE

TELEMAC-3D: keyword VELOCITY VERTICAL PROFILES available when prescribing
velocities at open boundaries (and not only flow rates)

BIEF: new formulation U.grad(psi) U.grad(F) for vector in Finite Elements in 2D

TELEMAC-3D: read bottom friction from the FILE FOR 2D CONTINUATION rather than
from the GEOMETRY FILE if 2D CONTINUATION = YES

TELEMAC-2D/TELEMAC-3D: fix securing HBOR to be positive (tide + TOMAWACT3D)

GAIA: RESTART MODE for GAIA like in TELEMAC-2D and TELEMAC-3D

GAIA: Add a feature to skip bed updates in a first period of the simulation.
New keyword: SPINUP TIME FOR BED UPDATING.

TELEMAC-3D: TELEMAC3D was not correctly giving the wind to TOMAWAC.
It was using TOM2TEL instead of TEL2TOM.

Python: Fix url of Corine Land Cover (CLC) database and possibility to use
latest CLC data from 2018 (as default now) instead of 2012.

The SISYPHE module has been removed from the system.

GAIA: the following keywords are deleted since not used:
NUMBER OF SUB-ITERATIONS, THETA IMPLICITATIONS FOR SUSPENSION.
Remove choice 2 for keyword SCHEME FOR DIFFUSION OF SUSPENDED SEDIMENTS IN 3D
("VERTICAL DIFFUSION ONLY").

TELEMAC-3D: remove choice 2 for keyword SCHEME FOR DIFFUSION OF TRACERS
as useless ("VERTICAL DIFFUSION ONLY")

TOMAWAC: Continue to make a linear temporal interpolation for the wind or
the tidal informations, even when you continue a computation.

KHIONE: If snow is given in the meteo file, it is used directly in the
thermal module, instead of being computed after the visibility value

Python: Add features to MascaretGeoFile class:
 - reading topo-bathy information,
 - reading sediment layers in Courlis geometry files,
 - new method to generate GIS file formatted for PreCourlis QGIS plugin.
Modification of Section (class of mascaret_file.py) to store topo-bathy data

GAIA: new user subroutines for settling velocities and hindered formulations.

TOMAWAC: Default value of keyword STATIONARY WIND is changed to .FALSE.

TOMAWAC: Stop the calculation if a stationary wind is given in the TOMAWAC
steering file while coupled with TELEMAC2D/3D.

TOMAWAC: Keyword NEXT COMPUTATION was not read and not used it is deleted from
dictionnary.

GAIA: update for morphological factor, changes:
- keyword MORPHOLOGICAL FACTOR ON BED EVOLUTION is replaced by MORPHOLOGICAL
FACTOR
- keyword MORPHOLOGICAL FACTOR ON TIME SCALE is removed
- new keyword OUTPUT TIME FOR MORPHOLOGICAL FACTOR

GAIA: coefficients of Swart formula are now equal to the ones of the original
formula, without any truncation.

GAIA: the keyword MINIMAL VALUE OF THE WATER HEIGHT is now used to set
the deposition rate at zero (before: only erosion rate was set to zero
according to this keyword).

GAIA: add Apsley and Stansby formulation for slope effect as well as for
sliding. New test case to check sliding. Keyword SEDIMENT SLIDE is now an
integer.

GAIA: fix index shift for ALIRE array (COMPUTATION CONTINUED)

GAIA: fix bug for FLOCCULATION FORMULA and HINDERED SETTLING FORMULA. These
keywords were not read in GAIA

GAIA: fix units for CVSM serafin output file.

GAIA: fix the CVSM output period for output of specified nodes in order to
respect the value set in the steering file.

Python: fix TelemacFile.meshz so that it actually returns the Z coordinates.

TELEMAC-2D: add failure criteria for breach initiation.

STBTEL: fix an issue when interpolating with 4 bathymetry files.

GAIA: fix a coefficient in the bedload formulas of Engelund-Hansen
according to the value given by the literature.

Python: Telapy for TELEMAC-2D RESTART MODE

TELEMAC-2D: Fortran API for RESTART MODE for perfect restart

TOMAWAC: add frequential ratio, number of frequencies and directions,
energyspectrum and variables to deal with white capping in api.

Python: Matrix dimension problem fixed for TELEMAC-2D matrices in TelApy.

TELEMAC-2D/TELEMAC-3D: fix bug with MOD if RESTART FILE PRINTOUT PERIOD = 0
for gfortran 10.2.1 with debug options

TELEMAC-2D/TELEMAC-3D: fix bug when adding particles (no need to compute
if through an open boundary)

TELEMAC-3D: fix bug when computing ZFLOT in sequential for drogues

TELEMAC-3D: wrong computation of global number index of node in BORD3D
in parallel

GAIA: fix bug for bed model with consolidation when computation continued

TELEMAC-3D: enable stochastic diffusion model to be activated by keyword
STOCHASTIC DIFFUSION MODEL for particle tracking with drogues

Python: missing argument in the call to set, in the function mpi_set from
TelApy.

Release V8P4R0 (01/12/2022)
===========================

Python: all Python MASCARET and COURLIS cases now run properly on Windows.

COURLIS: fix for SARAP kernel that is doing a first timestep with zero
duration for its initialization that was problematic for COURLIS (the call
of COURLIS is now deactivated in this case)

TOMAWAC/API: added new TOMAWAC API variables.

GAIA: in case of active layer+consolidation no sliding is possible for
active layer. Sliding will be possible from layer 2.

GAIA: fix bug with bed model in case of active layer and consolidation.

GAIA: fix for time used to compute erosion between layers.

GAIA: fix for mud concentration, confused with mud concentration of
active layer in some cases.

Python: all notebooks now run properly on Windows. The following test
cases have also been fixed to run on Windows:
- vnv_build_srf.py
- vnv_mascaret_convert_xcas_cas.py
- vnv_api_mascaret.py
- vnv_hermes.py
While also fixed, vnv_api.py and vnv_coupling.py do not run on Windows yet
because of other issues. The same applies to other test cases that are still
failing.

TELEMAC-2D: change the keyword INITIAL LENGTHS OF BREACHES to
INITIAL WIDTHS OF BREACHES to be coherent with literature and manual.

Courlis: fix inconsistencies on keywords between dico_courlis.txt
 and mascaret.dico

GAIA: fix update of thickness and bottom after suspension and sliding.

KHIONE: Change thermal growth boundary layer to thickness instead of radius,
and updated thermal growth default calibrated parameters accordingly.
Fix heat budget in presence of ice cover.
Add Morse and Richard 2009 rise velocity formulation.
Add porosity of surface ice in mass exchanges between frazil and ice cover.
Add buoyancy velocity and static ice cover implementations for coupling
with TELEMAC-3D.

Python: add tif processing and tif to slf fonctionnality

Python: fix bug with interpolation.
add nearest interpolation when tri interp returns NaN

Python: fix a crash occuring on Windows when using run_refine from
stbtel_refine.py.

GAIA: fix sources terms (Qsce*Tsce) of advection-diffusion eq. were not
included in the resolution of the equation

Python: Add an option to points_in_poly and set_data_in_poly to have a
tolerance to determine if a point is in a polygon.

Python: fix temporary folder was not deleted in HPC runs

GAIA: fix wrong use of AC and DCLA

Python: fix problem in TelemacCas Python class for long path file string in
steering file.

Python: it is now possible to make a local refinement with converter.py
refine option by giving a GIS file containing one polygon (.shp file for
example)

STBTEL: Algorithm to detect nodes inside a given polygon has been replaced
 by bief inpoly function to avoid limitation for concave polygons.

TELEMAC-2D: fix no prescribed tracer value to be given for secondary currents
at open boundaries

TELEMAC-2D: fix update of UCONV and VCONV when ADVECTION = NO

Python:
- manip_telfile.py: merge function now works properly, sorts time records and
avoids duplicates.
- TelApy: use the size function instead of shape to obtain the overall size of
knolg in l2g.
- TelemacFile: fix wrong boundary point detection in add_bnd.
- clc.py: update URL of Corinne Land Cover servers.

TELEMAC-3D: add tracer viscosity computation for Spalart-Allmaras model

TELEMAC-3D: Prandtl number available for k-omega and Smagorinski models

TOMAWAC: Allocate wind array in point_tomawac.f when there is a formatted
file for the wind.

TOMAWAC: Initialize current in case of tide in case there would not be any
current in tidal file

Python: the compilation system has been fixed to use a more standard way of
linking library. This fixes Linux binaries generation in dynamic mode and
removes the need to specify "dyn" or "static" as a build option.

TELEMAC-3D: Transform 3 keywords to arrays:
- ACCURACY FOR DIFFUSION OF TRACERS
- MAXIMUM NUMBER OF ITERATIONS FOR DIFFUSION OF TRACERS
- OPTION OF SOLVER FOR DIFFUSION OF TRACERS

Python: GRETEL method for merging data can now be specified through runcode.py.

TOMAWAC: fix results of coupling with TELEMAC3D change with graphic output
period

Python: new --project option to specify the project to use for an HPC job.

WAQTEL: fix wrong 3D equations in WAQTEL for O2, BIOMASS and EUTRO

TELEMAC-2D/TELEMAC3D: fix possible negative values under square roots for
culverts

TOMAWAC: Define area of Porous media and vegetation through polygones read in a
text file, add keywords in dictionnary to define vegetation characteristics

TELEMAC-2D/TELEMAC-3D: new constituents 2Q1 and M3 taken into account
for TPXO9v5 tidal solution + fix S1 formulae

TELEMAC-3D: new keywords for RESTART MODE as done in 2D:
  - RESTART FILE PRINTOUT PERIOD
  - RECORD NUMBER IN RESTART FILE

TELEMAC-2D/TELEMAC-3D: new default value for RECORD NUMBER FOR RESTART
= -1 (old default value = 0) to enable to use initial conditions

TELEMAC-2D: RESTART MODE for perfect restart as in 3D

TELEMAC-2D: Adding new infiltration model : Green-Ampt and Horton in runoff routines

TOMAWAC: Cache Optimisation for qdscur.f (opposing current)

TOMAWAC: coupling TELEMAC-3D and TOMAWAC with tel2tom, test cases added in
3Dcoupling.

TELEMAC-2D: fix sources defined by regions in parallel when belonging to
several subdomains

TOMAWAC: When TOMAWAC is coupled with TELEMAC-2D or TELEMAC-3D the wind taken
into account in TOMAWAC is the one coming from TELEMAC-2D or TELEMAC-3D

TELEMAC-2D: fix parallel/sequential differences with tidal flats
and no friction

WAQTEL: two-step reversible kinetics model in WAQTEL-MICROPOL
  - Adds the keyword KINETIC EXCHANGE MODEL to choose between one or two steps kinetic exchanges
  - Adds new tracers when kinetic 2 model is chosen
  - Updates the way WAQTEL NAMETRAC is called in TELEMAC-2D/3D
  - Adds new test cases for kinetic 2 exchanges in 2D and 3D

TOMAWAC : Take into account keyword : TIME INCREMENT NUMBER IN TELEMAC FILE.
last time step otherwise

All modules: fix double precision needed in DATE_MJD2SEC (time relative in input files)

TELEMAC-2D: fix Huthoff vegetation friction law (minimum between water depth and vegetation depth)

TELEMAC-2D: change DRAGFO to user subroutine (sources + dragforce example)

TELEMAC-2D: fix friction laws defined by areas (FRICTION DATA = YES) with Finite Volumes

WAQTEL: updated source code for sediment transport in MICROPOL 3D
  - Adds suspended sediment and bed sediment exchanges with diffusion source term in the bottom layer
  - Corrects the suspended sediment tracer to effectively fall trough the layers with the corresponding velocity
  - Adds new test cases for sedimentation and erosion
  - Fixes pollutant tracers for transport in suspended and bed sediments
  - Adds new test cases for pollutant-sediment interactions

TELEMAC-2D: fix Dirac sources or culverts belonging to several subdomains in parallel

TELEMAC-3D: fix TRACERS VERTICAL PROFILES = 0 possible if tracer is not sediment

TOMAWAC: set TOMAWAC constants in declarations_tomawac.

TELEMAC-2D: fix sources of tracers with Leo Postma advection scheme (= 3)

TOMAWAC: Add developments on reflection in Tomawac, documentation and one test case

GAIA: bug fix Soulsby Slope effect (SLOPEFF=2) available for all threshold formulas (before only MPM)

TELEMAC-3D/WAQTEL: fix negative concentrations with TELEMAC-3D/WAQTEL coupling

GAIA: fix final GAIA balance written at last time step even if not a multiple of
LISTING PRINTOUT PERIOD

TELEMAC-3D: fix RESTART FILE not well written if NUMBER OF TIME STEPS is not a
multiple of GRAPHIC PRINTOUT PERIOD

TOMAWAC : Correction of a bug occuring in a COMPUTATION CONTINUED case with
          current.

WAQTEL: updated example test cases and documentation for MICROPOL (2D):
  - Added 5 test cases to assess each set of equations for sorption, desorption, decay and sedimentation
  - Updated documentation with units and more thorough explanations

PYTHON: several issues are fixed
 - The ASCII banner now correctly displays the version when using released sources
 - TELEMAC-MASCARET can be compiled on Windows in dynamic mode
 - User Fortran DLLs are unloaded on Windows
 - stbtel_converter.py is not crashing anymore on Windows

TELEMAC-2D: inserting hybrid vegetation law
 - updating the vegetation test case to include hybrid vegetation law

TELEMAC-2D: bug fix Lindner subroutine
 - lambda needs to be calculated including CF, because it is used in the iteration procedure.

TELEMAC-3D: Fix writing 2D RESULT FILE in longitude/latitude

MASCARET: python scripts have been added to convert DAMOCLES steering file into
  XML MASCARET steering files (and vice versa) (added actually in V8P3R0)
 - A new MASCARET-TRACER-COURLIS dictionnary including all tags and keyword has been added
 - Python script mascaret_cas.py has been modified for the conversion (based on TelemacCas
Python class)
 - mascaret.py (runcode.py) running script has been also adapted to run a calculation equally
with a DAMOCLES steering file or a XML steering file (only for MASCARET-TRACER, COURLIS is
still using only DAMOCLES steering file)

MASCARET: New scheme option for SARAP kernel (added actually in V8P3R0)
 - XML tag: "decentrement"
 - DAMOCLES keyword: UNCENTERED SCHEME

COURLIS: 3 bedload formulas have been added (added actually in V8P3R0)
 - Lefort 2014, Recking 2013 and Recking 2015
 - New keyword: BEDLOAD TRANSPORT LAW (+ 2 keywords for Recking 2015)

COURLIS: Documentation has been added (added actually in V8P3R0)
 - User documentation
 - Reference documentation (based on MASCARET-TRACER-COURLIS new dictionary)
 - Theory documentation (WIP)

COURLIS: New option in bedload module for boundary condition, equilibrium bedload
  discharge at upstream defined by a slope and the selected bedload formulas (added
  actually in V8P3R0). Two new keywords:
 - UPSTREAM SEDIMENT CONCENTRATION FROM EQUILIBRIUM SLOPE
 - UPSTREAM EQUILIBRIUM SLOPE

Release V8P3R0 (06/12/2021)
===========================

GAIA: fix CSRATIO computation, now allocated as block of vectors.

TELEMAC-2D: Non-newtonian models implemented.
 - New keywords: NON-NEWTONIAN MODEL, BINGHAM OPTION,
NON-NEWTONIAN VISCOSITY, NON-NEWTONIAN YIELD STRESS,
NON-NEWTONIAN LAMINAR RESISTANCE PARAMETER K,
NON-NEWTONIAN PSEUDO-BIPHASIC MODEL, NON-NEWTONIAN FLUID DENSITY,
HERSCHEL-BULKLEY POWER-LAW INDEX.
 - New test cases: nn_newt directory testing the implementation
of the model and its accuracy vs analytical solution and the
implementation of a pseudo biphasic model
 - This feature is only available in the finite volume kernel of
TELEMAC-2D because of instabilities at the wet/dry interfaces
with finite elements

TELEMAC-2D: finite volume update.
Splitting volfin in two parts to compute the good time step,
used in some source terms and Thompson boundary conditions.

GAIA: change and fix the convention for wave and current direction in GAIA:
in degree and trigonometrical (wrt x-axis). New keyword (TRIGONOMETRICAL
CONVENTION IN WAVE FILE) to define if the nautical or the trigonometrical
convention is used in the TOMAWAC results file (to be defined only in case
of reading this file without COUPLING WITH = TOMAWAC).

KHIONE: major update
  - Coupling with TELEMAC-3D (tracers and thermal budget)
  - Mass-exchanges between suspended frazil ice and ice cover in 2D
    with new test case (mass_exchanges-t2d) and user documentation
  - Ice cover dynamics in 2D (part 1: advection of ice cover thickness
    and surface fraction + thermal expansion and decay)
  - New logic for flux limitors in frazil explicit sources
  - New test case for border ice (saint_lawrence-t2d)
  - New test cases with comparison to experimental data
    for both mono-class and multi-class models i.e. racetrack_carstens-t2d
    and racetrack_tsanghanley-t2d
  - Seeding rate changed from volumic to surfacic
  - New default value for keywords: FRAZIL CRYSTALS RADIUS,
    MINIMUM NUMBER OF FRAZIL CRYSTALS, FRAZIL SEEDING RATE
  - Ice cover pressure gradient momentum source term
  - Ice cover friction composite law
  - Radiative flux penetration as a function of turbidity
    (when coupling with TELEMAC-3D)

GAIA: fix options for bed roughness predictor. Inconsistency between dictionary
and subroutine.

TELEMAC-2D: new laws for breaching processes. A description is given in the user
doc. The breach test case has been updated with these new laws.

TELEMAC-2D/TELEMAC-3D: new keyword to define if the format of an ASCII or BINARY
ATMOSPHERIC DATA FILE is free to be handled outside the METEO_TELEMAC module

WAQTEL: fix bug of degradation law combined with another WAQTEL module in 2D

TELEMAC-2D: finite volume update.
  - New schemes available to solve diffusion problems with the finite volume framework:
      1. Explicit P1 finite element with mass lumping (default),
      2. TFP (Two Point Flux) finite volume scheme,
      3. RTFP (Reconstructed Two Point Flux) finite volume scheme.
  - The new schemes are available for both velocity and tracers and can be selected with the keywords:
      - 'FINITE VOLUME SCHEME FOR VELOCITY DIFFUSION'
      - 'FINITE VOLUME SCHEME FOR TRACER DIFFUSION'
  - Implementation of a Fourier condition on time step to satisfy the diffusion
    stability condition (similar to the CFL condition).
    Can be adjusted with the new keyword 'DESIRED FOURIER NUMBER' (1. by default).
  - New keyword: 'OPTION FOR DIRICHLET CONDITION IN FV DIFFUSION' allowing choosing
    weak or strong imposition of the Dirichlet condition in the diffusion flux.
  - Two versions are implemented for the RTPF scheme reconstructions which can be
    selected via the new keyword 'OPTION FOR THE RTPF SCHEME RECONSTRUCTIONS'
      1. Reconstructions with subcell gradients (default),
      2. Reconstructions with cell gradients.
  - Update of the finite volume documentation.
  - New test cases for the validation of the finite volume diffusion schemes:
    cone_diffusion, tracer_diffusion, tracer_diffusion_convergence.
  - Fix major bug on inlet boundary condition for the advection schemes.

TELEMAC-2D/TELEMAC-3D: new keyword STAGE-DISCHARGE CURVES RELAXATION COEFFICIENT

GAIA: fix bug in active layer concentration for mud.

TOMAWAC: changing lecdon_tomawac to have more than 72 characters to define variables of output (250).

PYTHON: tel2tom deals with exclusion of contour in the construction of interpolation. New tests cases added to test it in case littoral.

PYTHON: the boundary file was not transmitted to tel2tom which makes partel stop in parallel. An error in interpolation was made in pretel.

TOMAWAC: Type INTEGER for variable HDC could not stock number of hours in a date. It has been changed to KIND=K8.

TEL2TOM fix solves a segfault (probably only important with one processor).

TELEMAC-3D: fix bug for CHECKING THE MESH = YES with prisms

TELEMAC-3D: fix arguments mismatch for advection of sediment with settling velocity

All modules with binary meteo data: error of index when initialising BINARY ATMOSPHERIC DATA FILE
in METEO_TELEMAC module

GAIA: fix call to PREP_ADVECTION_GAIA in TELEMAC2D with good array of advection
schemes ICONVFT

TELEMAC-2D, TELEMAC-3D, GAIA, WAQTEL, KHIONE: fix no check between
number of tracers and MAXIMUM NUMBER OF TRACERS

GAIA: fix for suspension in 2D. Advection field for suspension is now selected
according to SOLSYS.

WAQTEL: fix bug wrong reading of the 2nd component of the keywords 2 keywords
COEFFICIENTS OF ALGAL MORTALITY AT 20C and ALGAL TOXICITY COEFFICIENTS
(for BIOMASS and EUTRO models)

all modules with meteo data: fix bug for y component of wind in METEO_TELEMAC module

ARTEMIS : fix bug reading of the correct names of variables in a tomawac output spectrum results file.

GAIA: fix bug reading PRESCRIBED SUSPENDED SEDIMENTS CONCENTRATION VALUES
in 2D and 3D and when reading COEFFICIENT FOR HORIZONTAL / VERTICAL DIFFUSION
OF SUSPENDED SEDIMENTS in 3D

GAIA: fix bug arising in cases where TELEMAC-3D is coupled with GAIA for
bedload and other tracers are activated in TELEMAC-3D

WAQTEL: fix bug reading of COEFFICIENTS OF AERATION FORMULA (THERMIC module)

TOMAWAC: a new output is able, the white capping rate through the keyword BETAWC

GAIA: fix deallocation issue with advection velocity

PYTHON: equivalent of diff_selafin.py now possible for all telemac file formats in run_telfile.py diff_ascii


Release V8P2R0 (01/12/2020)
===========================

WAQTEL: fix the initialisation of AED2 extinction coefficient for crushed nodes

TELEMAC-2D: fix bug in sources when given by regions and only velocity is
assigned

GAIA: fix bug in restart mode concerning CO sediments

WAQTEL: fix the bug of negative concentrations when coupling TELEMAC-3D with AED2

WAQTEL: erosion flux computation with MAX not ANTI_DIRAC function when
wetting/drying for MICROPOL module

WAQTEL: 2 bottom tracers are to be not advected nor diffused with MICROPOL
module

WAQTEL: swap of indices between keywords SEDIMENTATION CRITICAL STRESS and
CRITICAL STRESS OF RESUSPENSION for MICROPOL module

WAQTEL: light extinction coefficient can be directly given as constant
(THERMIC, BIOMASS + EUTRO models)

TELEMAC-2D: New version of WEIRS TYPE = 2 weirs, fully parallelized with Tracer.

GAIA: new keywords for sediments, CVSM model added to Gaia, new listing output
for sediments mass balance (and tracers), new test cases, new postel function
to extract sediment mass information, new structure for the user doc but still
work in progress.

DOCUMENTATION: Updated doxygen for sources and Python. Notebooks will also be
avaialble in html format (documentation/notebooks/index.html)

PARAVIEW: New version of Paraview plugin now handling double precision and
fixes the issue with VELOCITY vectors and handling more vectors.

TELEMAC-2D/TELEMAC-3D: Time reference in all Telemac2d/3d time related files:
You can add #REFDATE in the ascii files and the date will be added to the times
in the files when used in Telemac2d/3d. For SERAFIN/MED it will use the date in
the file.

PYTHON: New functionalities for pre-treatment (mainly in folder pretel):
  - New set of functions to write/modify a file (See notebook
    data_manip/extraction/telemac_file.ipynb)
  - Python version of the MATLAB script that computes weight to interpolate
    between two mesh (for Tel2Tom coupling)
  - Adding support for fiona in the shapefile_reader function:
  - Extraction of contour (Shapefile) from a mesh file (with and without
    boundary file) works when you have islands, separated domains... (see notebook pretel/extract_contour.ipynb)
  - Converter shapefile to ascii/i2s(See notebook data/manip/extraction/shape_file_reader.ipynb):
  - New structure/scripts for interpolation (list of points on mesh) (see notebook pretel/interpolation*).
  - Difference between steering files (See notebook execution/steering_file.ipynb)
  - Corine Land Cover extraction (See notebook pretel/corine_land_cover.ipynb)
  - Check time coherance in inputs files (See notebook execution/steering_file.ipynb)
  - Mesh Quality in run_selafin.py check:
        Check for isolated point.
        Compute Circle ratios.
        Number of elements around a node.
        Elements angles.
        Over-constrained nodes.

TELEMAC-2D: keyword COEFFICIENT FOR DIFFUSION OF TRACERS is now an array not a
single value (i.e. one value per tracer) like in 3D

TELEMAC-2D/TELEMAC-3D/SISYPHE/GAIA: new default values for:
MAXIMUM NUMBER OF ITERATIONS FOR ADVECTION SCHEMES = 50 (old default value = 10)
MAXIMUM NUMBER OF ITERATIONS FOR POSITIVE THICKNESS = 50 (old default value = 10)

WAQTEL: keyword COEFFICIENT OF CLOUDING RATE now available for heat exchange
with atmospheric (THERMIC) module in 3D + new default value = 0.17, old = 0.2

TELEMAC-2D/TELEMAC-3D/WAQTEL/KHIONE: flexible format for ASCII ATMOSPHERIC
DATA FILE + new module for meteo variables METEO_TELEMAC

TOMAWAC/TELEMAC2D : push into the trunk the coupling between tomawac and
telemac2d called tel2tom, it allows coupling on different meshes. To use it
just change the value of coupling with 'tomawac2' in the telemac2d keyword

ARTEMIS: Deleted keywords
  - DISCRETIZATION IN SPACE
  - LAW OF BOTTOM FRICTION
  - MINIMUM VALUE FOR H
  - RELAXATION COEFFICIENT
  - GEOMETRY FILE BINARY
  - RESULTS FILE BINARY
  - GEOMETRY FILE STANDARD
  - RESULTS FILE STANDARD
  - USER CRAY
  - PRIORITY
  - ACCOUNT NUMBER
  - BIDON STRING
  - LIBRARIES

WAQTEL/TELEMAC-3D: fix missing light extinction coefficient in the coupling with
AED2, to be added to other extinction coefficients computed by AED2

WAQTEL/TELEMAC-3D: fix one single call of penetration of solar radiation
when coupling TELEMAC-3D with AED2

WAQTEL/TELEMAC-3D: fix wrong indices of WAQPROCESS for check or error messages

WAQTEL: fix a bug with linearised formula for heat exchange model:
no penetration of solar radiation with this linearised formula (only located
at the surface)

TELEMAC-3D: fix a bug with BINARY BOUNDARY DATA FILE, local indices have to be
used, not global indices with working arrays T3_01

TELEMAC-3D: new keyword to change the number of tracer used for AMR
(MESH TRANSFORMATION = 5)

WAQTEL: new keyword to read the solar radiation in the meteo file instead of
computing it in the heat exchange with atmosphere module in 3D

TELEMAC-2D/TELEMAC-3D: possibility to use x and y origin coordinates stored
in the geometry file to decrease the number of digits of coordinates
when modelling tide.
The tidal computations automatically take into account this offset for
UTM + Lambert projections for JMJ+OSU (e.g. TPXO) databases
Deleted keyword: ORIGIN COORDINATES

TELEMAC-2D/TELEMAC-3D new keywords to define the minimum water depth by which
divisions of transports are done for boundary and initial conditions if using
OSU tidal solutions (e.g. TPXO) + possibility to start with 0 velocity
or velocity computed by OSU tidal solutions

TELEMAC-3D: UBOR2D and VBORD2D arrays not filled in correctly
for Thompson Boundary Conditions in 3D

TELEMAC-3D: COEFFICIENT TO CALIBRATE TIDAL VELOCITIES really taken into account
when modelling tide in 3D (all tidal databases)

WAQTEL: possibility to use a wind function with 2 calibrating coefficients
with ATMOSPHERE-WATER EXCHANGE MODEL = 2 in 3D

WAQTEL: new degradation laws for 2D and 3D (classical 1st order degradation law,
not only bacterial T90 laws) + possibility of user defined degradation law

TELEMAC-3D: fix the reading of STAGE-DISCHARGE CURVES FILE in 3D

KHIONE: fix static border ice criteria, fix clogging model,
new logic for ice processes, remove ice cover dynamics obsolete developments,
remove coupling with waqtel, add new keywords for frazil ice thermal growth
and thermal budget, new semi-implicit source for frazil thermal growth,
new multiclass frazil ice model with thermal growth and decay,
secondary nucleation, flocculation, precipitation, salinity effects and turbulence

TELEMAC-2D: adding a variable ADR_TRAC (address of tracers) for TELEMAC-2D
rather than using multiple hard-coded values

TELEMAC-3D: fix keeping longitude/latitude coordinates writing with TELEMAC-3D

TELEMAC-2D+TELEMAC-3D: new keyword to tell if bottom smoothings are to be done
after or before user modifications of bottom:
BOTTOM SMOOTHINGS AFTER USER MODIFICATIONS

TELEMAC-3D: velocity components + tracers values at the free surface as
variables for graphic printouts of the 2D RESULT FILE

PARALLEL: new generic function:
Function that had the same functionalities but different argument types can now be called using the same function.
For example instead of using p_imax, p_dmax you use p_max for both case.
  - P_IMAX, P_DMAX => P_MAX
  - P_IMIN, P_DMIN => P_MIN
  - P_ISUM, P_DSUM => P_SUM
  - MPI_ADDRESS1, MPI_ADDRESS2, MPI_ADDRESS3 => MPI_ADDRESS
  - P_IMAX_ARRAY, P_DMAX_ARRAY => P_MAX_ARRAY
  - P_MPI_ALLTOALLV_I, P_MPI_ALLTOALLV_OIL, P_MPI_ALLTOALLV_ALG, P_MPI_ALLTOALLV_CHARAC => P_MPI_ALLTOALLV
  - P_DREAD, P_IREAD, P_IREADI8, P_IREADI => P_READ
  - P_DWRIT, P_IWRIT, P_IWRITI8, P_IWRITI => P_WRITE

TELEMAC-2D: new vegetation friction laws

Python: New script manip_cas.py to check/sort you steering file

TELEMAC-2D: fix restart mode with tracers (T1 was missing)

TELEMAC-3D: fix the overwriting of TELEMAC-3D boundary conditions when coupling
with TOMAWACT3D

TELEMAC-3D: fix for RESTART FILE with NON-HYDROSTATIC VERSION = NO

TELEMAC-2D: new default values for 3 keywords:
  - TREATMENT OF THE LINEAR SOLVER = 2 (i.e. wave equation, old = 1: coupled),
  - COEFFICIENT OF WIND INFLUENCE VARYING WITH WIND SPEED = YES,
  - COEFFICIENT OF WIND INFLUENCE = 1.55E-6 (rather than 0.).

TELEMAC-2D: New finite volume architecture

TELEMAC-2D: new keyword to calibrate the 2D mixing length turbulence model
  - MIXING LENGTH MODEL COEFFICIENTS

TELEMAC-3D: new default value for keyword COEFFICIENT OF WIND INFLUENCE VARYING
WITH WIND SPEED = YES (old = NO)

TELEMAC-3D: new keywords
  - MINIMUM VOLUME OF 3D ELEMENTS
  - MINIMUM DISTANCE BETWEEN PLANES CLOSE TO THE BOTTOM
  - MINIMUM DISTANCE BETWEEN PLANES CLOSE TO THE FREE SURFACE
  - THRESHOLD HEIGHT BEFORE CRUSHED ELEMENTS

TELEMAC-3D: fix the reading of BINARY BOUNDARY DATA FILE and the computation
of HBOR using it in BORD3D

TELEMAC-3D: fix the bad initialisation of wave variables transmitted to GAIA
in case of triple coupling TELEMAC-3D+TOMAWAC+GAIA

TELEMAC-3D: fix of wrong argument when calling CVDF3D with Spalart-Allmaras or
DES turbulence models, now connected to a k-epsilon model parameter

TELEMAC-3D: Deleted keywords
  - 3D RESULT FILE BINARY
  - 2D RESULT FILE BINARY

TELEMAC-2D: Deleted keywords
  - PSI SCHEME OPTION
  - PROPAGATION OPTION
  - UPWIND COEFFICIENTS
  - TIME STEP REDUCTION FOR K-EPSILON MODEL
  - COUPLING DIRECTORY

TOMAWAC:
  - Changing name of variables in spectrum file now FXXXXXPT2DXXXXXX (for
example F00001PT2D000303)
  - BAJ modeling does not include non linear quadruplet anymore.

Doc: Adding html version of notebooks in documentation/notebooks. In trunk run
doc_telemac.py -M notebooks to generate it. In release it will be there.
Run firefox $HOMETEL/documentation/notebooks/index.html to see it.

KHIONE: fix a wrong call of VECTOR in border_icover

WAQTEL: fix an unexpected division by 0 in calcs2d_micropol (OVD)

MASCARET: Make editable the laws of singularity and add variables in api:
ControlSection and MaxcontrolZ

TELAPY: Add python files and examples for mascaret/telemac-2d coupling
        Add python files and examples for mscaret/telemac-2d drivers for
	  data assimilation and UQ

TELEMAC3D: COUPLING WITH changing default from 'NOTHING' to ''

TELEMAC 3D: Fix missing PARCOM (volumetric explicit source terms) if LIPS advection
scheme is used.

ALL: Removing SERAFIN? file format option

TELEMAC 3D: Fix missing term (volumetric sources) in the computation of the balance
for the tracers. This fixes wrong thermal balance in case of exchanges with atmosphere.

GAIA: fix a bug when sliding in parallel computations

TELEMAC-2D: Drogues can be defined using a polygon file and in the geometry file.
Drogues can be output to a binary (PCL) file which can be read by BlueKenue.

TELEMAC-2D: Algae classes can be defined and different Algae properties can be defined
for each class. The Algae can start to move after a specified time has elapsed.
Alternatively Algae can start to move after being dislodged after a critical bed
wave orbital velocity has been reached.

TELAPY: New function mpi_get, mpi_get_array (and set equivalent) to get array
over global mesh

TELAPY: New functions read/write for TelemacFile to modify a file.
See notebook notebooks/telapy/telemac_file.ipynb for examples.

Release V8P1R0 (04/12/2019)
===========================

WAQTEL: fix the differences between source code and documentation for EUTRO, MICROPOL(2D)

TELEMAC-3D: rewriting of one loop for Automatic Mesh Refinement (aka AMR or
MESH TRANFORMATION = 5) to reduce the differences between sequential and parallel

WAQTEL: fix the wrong formula for air specific moisture in CALCS2D_THERMIC

WAQTEL: fix the Churchill formula for the computation of the reaeration coefficient K2
for O2 and EUTRO

TELEMAC-3D: fix inconsistency between boundary conditions in the matrix
(mass-lumped form) and in the right-hand side (lateral and free surface boundary
conditions was impacted).

WAQTEL: new theory guide + user manual completed

WAQTEL/AED2: fix the bug of wrong computation of array BENTH4AED2
+ wrong location of the fluxes transmitted to TELEMAC-3D

TELEMAC-2D/TELEMAC-3D/WAQTEL: fix the bug of expected format when using at the same time
WAQTEL + WIND = YES + OPTION FOR WIND = 2 with an ASCII ATMOSPHERIC DATA FILE

TELEMAC-2D/TELEMAC-3D: fix the bug of unexpected choice for ZONE NUMBER IN GEOGRAPHIC SYSTEM

TELEMAC-3D: New density law: Jackett et al. (2006)

TELEMAC-2D: New keyword COEFFICIENT OF WIND INFLUENCE VARYING WITH WIND SPEED

TELEMAC-2D/TELEMAC-3D: TPXO module: S1 constituent taken into account (for TPXO9)

PYTHON3: New validation system now using Python instead of xml structure. For
more information read the chapter "Validation" in the developer_guide

PYTHON3: New post treatment module postel. All the documentation can be found
in the notebooks to run them you jupyter notebooks and to lanuch the command
"jupyter notebook $HOMETEL/notebooks/index.ipynb"

WAQTEL: fix the bug for degradation law in 3D (WATER QUALITY PROCESS = 17)

TELEMAC-3D: Coupling of TELEMAC-3D with GOTM (standard GOTM)

TELEMAC-3D/SISYPHE: fix the bug of writing of results at the wrong graphic output

TELEMAC-3D/WAQTEL: fix the bug of wrong formula for the linearised formula
at the free surface for ATMOSPHERE-WATER EXCHANGE MODEL = 1

TELEMAC-3D: fix a bug with TKE computation with Spalart Allmaras turbulence model

GAIA : introduction of this new module, that aims at replacing both SISYPHE and SEDI3D.
  The goal is to have:
    - one sediment module only, instead of 2
    - one bed model for 2D and 3D, without limitations on the number of classes of
      sand and mud
    - the suspension fluxes computed in TELEMAC2D or TELEMAC3D depending on the
      dimension (resolution of a tracer equation)
    - all the sediment evolutions written in terms of mass (instead of volume)
    - no more standalone option for the 2D hydrodynamics inside the sediment module
  In this first version of GAIA, the major developments were:
    - to write the 2D/3D bed model based on the sediment fluxes writtent in
      terms of mass
    - to use that bed model and in 2D and 3D
    - to make it compatible with wave effects when coupling with waves
    - to implement the suspension in 2D inside TELEMAC2D, and modify it in 3D to
      comply with GAIA
    - to introduce the coupling between NESTOR and GAIA
  At this stage, SISYPHE and SEDI3D can still be used in the system, but we advise the users
  to switch and start using GAIA as soon as possible. Indeed, the plan is to remove SISYPHE
  and SEDI3D from TELEMAC after one year of transition with GAIA.

TOMAWAC : The components of the stokes drift, the wave enhanced mixing,
the wave dissipation due to bottom friction and wave breaking,
the modified friction coefficient due to waves are now calculated in respectively,
uvstokes, fdissk, fbott3d, fdiss3d and fric3d subroutines. This calculation allow to
have a full coupling with telemac3d through a vortex force formalism : COUPLING WITH TOMAWACT3D

TOMAWAC : A new tests case has been added to test this new functionnality :
          - 3Dcoupling

TELEMAC3D : - The variables calculated by tomawac are taken into account for a real 3D coupling.
            - 3 new output graphic variables are avalaible US, VS, WS the thress components of stokes velocity.
	    - One new keyword BOTTOM FRICTION DUE TO WAVES, it allows to take into account the momentum lost by waves due to bottom friction.

TELEMAC-3D: add one missing choice for output variables in telemac3d.dico
  - TAIR: air temperature (degree C).

TELEMAC-3D: Deleted keywords
  - SOLVER FOR VERTICAL VELOCITY
  - ACCURACY FOR VERTICAL VELOCITY
  - MAXIMUM NUMBER OF ITERATIONS FOR VERTICAL VELOCITY
  - PRECONDITIONING FOR VERTICAL VELOCITY

TELEMAC-3D: New default values for keywords
  - LAW OF BOTTOM FRICTION = 5 (old = 0 or 2), now mandatory to be given
  - FRICTION COEFFICIENT FOR THE BOTTOM = 0.01 (old = 60.), now mandatory to be given if any law of bottom friction
  - FRICTION COEFFICIENT FOR LATERAL SOLID BOUNDARIES = 0.01 (old = 60.)
  - SCHEME FOR ADVECTION OF VELOCITIES        = 5 (old = 1)
  - SCHEME FOR ADVECTION OF K-EPSILON         = 5 (old = 1)
  - SCHEME OPTION FOR ADVECTION OF VELOCITIES = 4 (old = 1)
  - SCHEME OPTION FOR ADVECTION OF TRACERS    = 4 (old = 1)
  - SCHEME OPTION FOR ADVECTION OF K-EPSILON  = 4 (old = 1)
  - IMPLICITATION FOR VELOCITIES = 0.55 (old = 1.)
  - SOLVER FOR PROPAGATION = 7 (old = 1)
  - SOLVER FOR PPE         = 7 (old = 1)
  - ACCURACY FOR PROPAGATION             = 1.E-8 (old = 1.E-6)
  - ACCURACY FOR DIFFUSION OF VELOCITIES = 1.E-8 (old = 1.E-5)
  - ACCURACY FOR PPE                     = 1.E-8 (old = 1.E-4)
  - ACCURACY FOR DIFFUSION OF K-EPSILON  = 1.E-8 (old = 1.E-6)
  - ACCURACY FOR DIFFUSION OF SEDIMENT   = 1.E-8 (old = 1.E-6)
  - OPTION OF SOLVER FOR PROPAGATION               = 5 (old = 3)
  - OPTION OF SOLVER FOR DIFFUSION OF VELOCITIES   = 5 (old = 3)
  - OPTION OF SOLVER FOR PPE                       = 5 (old = 3)
  - OPTION OF SOLVER FOR DIFFUSION OF K-EPSILON    = 5 (old = 3)
  - OPTION OF SOLVER FOR DIFFUSION OF TRACERS      = 5 (old = 3)
  - OPTION OF SOLVER FOR DIFFUSION OF THE SEDIMENT = 5 (old = 3)

SISYPHE: fix the bug of Finite Volumes in parallel

PYTHON: Now for some of the keywords that have restriction on their value
  (CHOIX or CHOIX1 in dictionary) the python script are checking that what you
  gave in your steering file is appropriate.

ALL: user fortran
  All user fortran have been replaced (except telemac2d/bord.f and sisyphe/conlit.f)
  by the same function prefixed with user_ by default they are empty (no code).
  You can still use the old ones but all the examples have been updated.
  Correspondance:
  - ARTEMIS:
      art_corfon -> user_art_corfon.f
      borh.F -> user_borh.f
      condih.f -> user_condih_particular.f
               -> user_condih.f
      fwspec.f -> user_fwspec.f
      utimp_art.f -> user_utimp_art.f
  - TELEMAC2D:
      analytical_solution.f -> user_analytical_solution.f
      bord.f -> user_bord.f
      condin.f -> user_condin.f
               -> user_condin_h.f
               -> user_condin_trac.f
               -> user_condin_uv.f
      corfon.f -> user_corfon.f
      corpor.f -> user_corpor.f
      corstr.f -> user_corstr.f
      debsce.f -> user_debsce.f
      def_zones.f -> user_def_zones.f
      flot.f -> user_flot.f
      href.f -> user_href.f
      lagran.f -> user_lagran.f
      maskob.f -> user_maskob.f
      mesures.f -> user_mesures.f
      nomvar_telemac2d.f -> user_nomvar_telemac2d.f
      preres_telemac2d.f -> user_preres_telemac2d.f
      q.f -> user_q.f
      sl.f -> user_sl.f
      source_telemac2d.f -> user_source_telemac2d.f
      trsce.f -> user_trsce.f
      utimp_telemac2d.f -> user_utimp_telemac2d.f
      vit.f -> user_vit.f
      vusce.f -> user_vusce.f
      vvsce.f -> user_vvsce.f
  - SISYPHE:
      cgl.f -> user_cgl.f
      condim_sisyphe.f -> user_condim_sisyphe.f
      conlit.f -> user_conlit.f
      cvsp_db.f -> user_cvsp_db.f
      init_compo.f -> user_init_compo.f
      init_compo_coh.f -> user_init_compo_coh.f
      maskab.f -> user_maskab.f
      mean_grain_size.f -> user_mean_grain_size.f
      noerod.f -> user_noerod.f
      predes.f -> user_predes.f
      qgl.f -> user_qgl.f
      qsform.f -> user_qsform.f
  - TELEMAC3D:
      bord3d.f -> user_bord3d.f
      condi3d_h.f -> user_condi3d_h.f
      condi3d_kep.f -> user_condi3d_kep.f
      condi3d_p.f -> user_condi3d_p.f
      condi3d_trac.f -> user_condi3d_trac.f
      condi3d_uvw.f -> user_condi3d_uvw.f
      driuti.f -> user_driuti.f
      flot3d.f -> user_flot3d.f
      impsed.f -> user_impsed.f
      kepini.f -> user_kepini.f
      limi3d.f -> user_limi3d.f
      mesh_transf.f -> user_mesh_transf.f
      preres_telemac3d.f -> user_preres_telemac3d.f
      q3.f -> user_q3.f
      sl3.f -> user_sl3.f
      source.f -> user_source.f
      t3d_debsce.f -> user_t3d_debsce.f
      t3d_corfon.f -> user_t3d_corfon.f
      t3d_trsce.f -> user_t3d_trsce.f
      tr3.f -> user_tr3.f
      tra_prof_z.f -> user_tra_prof_z.f
      utimp.f -> user_utimp.f
      vel_prof_z -> suer_vel_prof_z.f
      vit3.f -> user_vit3.f
  - TOMAWAC:
      anacos.f -> user_anacos.f
      anamar.f -> user_anamar.f
      anaven.f -> user_anaven.f
      couuti.f -> user_current.f
      dump2d.f -> user_dump2d.f
      limwac.f -> user_limwac.f
      maruti.f -> user_tide.f
      tom_corfon.f -> user_tom_corfon.f
      venuti.f -> user_wind.f
  - BIEF:
      corlat.f -> user_corlat.f
      corrxy.f -> user_corrxy.f
      strche.f -> user_strche.f

Release V8P0R0 (19/12/2018)
===========================

- Python3: Adding handling of MED format in vvytel now xml can handle both
  serafin and MED format
- Python: Work in progress new folder for scripts (scripts/python3) contains
  Python3 compatible scripts. All the scripts have been reorganised and renames
  to follow PEP8 convention. A new set of examples in examples/python3 show how
  to use them. Also a notebook exist showing how to use the postel module
  (Post-Treatment module).
  The folder scripts/python27 is kept for backward compatibility.
  All new development will be in the python3 folder.
- TelApy: Adding API for TELEMAC-3D
- TELEMAC-3D: New Spalart-Allmaras turbulence model. Together with a DES option which uses also Spalart-Allmaras model.
- TELEMAC-3D: new default values for 4 keywords:
  - NON-HYDROSTATIC VERSION = YES,
  - LAW OF BOTTOM FRICTION = 0 (rather than 2, Chezy law),
  - ACCURACY FOR DIFFUSION OF TRACERS = 1.E-8 (rather than 1.E-6),
  - COEFFICIENT OF WIND INFLUENCE = 1.55E-6 (rather than 0.).
- TELEMAC-3D: fix the uncorrect reading of private arrays when present in the GEOMETRY FILE (bug since V7P2).
- TELEMAC-3D: fix the reading of the binary boundary data file.
- TELEMAC-3D with AED2 coupling: partial fixes (wrong loops to sweep arrays, computation of the real number of the bottom layer...).
- SISYPHE: Implementation of the Wilcock and Crowe formula for sediment closure relationship
- SISYPHE: Add new test case (WC_BOMC4) to validate the Wilcock and Crowe formula; including python scripts. This test case also illustrates how to recirculate sediment in a straight channel (typically used in experimental flumes).
- SISYPHE: Add new section in documentation plus several improvements

Release V7P3R0 (22/12/17)
===========================

- all modules: FORTRAN FILE can be a folder that contains several files,
  not a single file (but still possible)
- TELEMAC-2D/TELEMAC-3D: fix the culvert formulation 1 so that
  it falls back to the siphon formulation in that specific case.
- TELEMAC-2D/TELEMAC-3D: sources can also be assigned with global node numbers
- TELEMAC-2D/TELEMAC-3D: Lambert 93 projection when modelling tide.
- TELEMAC-2D/TELEMAC-3D: Adding 7 extra harmonic constituents,
  for FES2014 tidal database (M3, M8, Msf, N4, S1, Sa, SSa).
- TELEMAC-3D: remove the option DIFFUS. This option was meant
  to remove the diffusion but it actually did not
  remove the diffusion on U,V. Besides, it could happen that when using
  DIFFUS=NO the source terms were not included in W and the tracers.
  We thus chose to remove this option altogether. From now on, to
  disable the diffusion the user can only set a zero diffusion coefficient.
- TELEMAC-3D: remove the option OPTDIF to keep only one formulation
  (OPTDIF could take the values 1 or 2 but the
  option 2 did not seem to bring improvements compared to the option 1.
  It was was not used in any test-case, neither documented so we only kept
  the option 1 in the code)
- TELEMAC-3D: modular CONDIM and BORD3D subroutines (initial conditions
  and boundary conditions). Simplification of the CONDIM subroutine
  (initial conditions + mesh transformation), now split into several
  subroutines which do various and separated treatments (e.g. initial
  conditions for water depths, velocities, tracers... or mesh
  transformation different from the classical sigma transformation).
  The user only needs to fill one short file per variable. No need to
  keep the whole CONDIM subroutine.
  For BORD3D, every specific treatment is implemented in a separate
  subroutine USER_BORD3D called by BORD3D (see examples to fill).
- ARTEMIS: Creation of free surface elevation (time/space varying) files.
- ARTEMIS: Removing the need to code within BORH (using LECLIM and
the BOUNDARY CONDITION FILE instead).
- ARTEMIS: Automated calculation of the phase for incident boundaries
  (in PHBOR), starting from the "node of attack" of the offshore wave,
  iteratively computed along both sides away from the attack node
  along the rest of the incident boundary.
- STBTEL: Now refining the boundary conditions as well as the mesh
  Available through the script convertert.py as well
- Addons: Adding vim-syntax for .cas and .dico files
- TELEMAC-2D: change computation of wall distance (used in
  Spalart-Allmaras turbulence model). The wall distance (WDIST) is now
  computed in parallel with a laplacian operator.
- TELEMAC-2D: new framework for automatic convergence studies
- TELEMAC-3D: coupling with the water quality library AED2.
- TOMAWAC: Automatic imposed spectrum on nested mesh.
- TOMAWAC: In order to better take into account boundary conditions Limwac is called at the end of the loop in time instead of beginning.
- TELEMAC-2D: I/O criteria of result file now homogenous with FE or FV (steered by time-step and
period for graphic output)
- TELEMAC-2D: Activation of source terms for FV (Mass and Momentum): so far only partially
implemented for mass source terms.
- TELEMAC-2D: New turbulence model (Spalart-Allmaras)

New keywords:
All modules:
For Automatic Differentiation (AD)
- AD NUMBER OF DERIVATIVES (AD NOMBRE DE DERIVEES)
- AD NAMES OF DERIVATIVES (AD NOMS DES DERIVEES)
- AD NUMBER OF DIRECTIONS (AD NOMBRE DE DIRECTIONS)
- AD SYMBOLIC LINEAR SOLVER (AD SOLVEUR LINEAIRE SYMBOLIQUE)
- AD LINEAR SOLVER RESET DERIVATIVES
(AD REMISE A ZERO DES DERIVEES DU SOLVEUR LINEAIRE)
- AD LINEAR SOLVER DERIVATIVE CONVERGENCE
(AD CONVERGENCE DES DERIVEES POUR LE SOLVEUR LINEAIRE)

TELEMAC-2D/TELEMAC-3D:
Keyword to assign global node numbers to sources:
GLOBAL NUMBERS OF SOURCE NODES (NUMEROS GLOBAUX DES NOEUDS DES SOURCES)
Keyword to give the coordinates of the result file in longitude-latitude
if the geometry file is also given in longitude-latitude:
RESULT FILE IN LONGITUDE-LATITUDE (FICHIER RESULTAT EN LONGITUDE-LATITUDE)
File to provide for the conversion in Lambert 93 for tides. It is
located in the tide examples of T2D (gr3df97a.txt):
LAMBERT 93 CONVERSION FILE (FICHIER DE CONVERSION LAMBERT 93)

TELEMAC-3D:
New keyword to compute the wind drag coefficient more accurately (FAIR):
- COEFFICIENT OF WIND INFLUENCE VARYING WITH WIND SPEED
(COEFFICIENT D INFLUENCE DU VENT DEPENDANT DE LA VITESSE DU VENT)

SISYPHE:
SECONDARY CURRENTS FILE (FICHIER DE COURANTS SECONDAIRES)

ARTEMIS:
FREE SURFACE ANIMATION (ANIMATION DE LA SURFACE LIBRE)
AMPLITUDE AND PHASE FILE (FICHIER DES PHASES ET AMPLITUDES)
AMPLITUDE AND PHASE FILE FORMAT
(FORMAT DU FICHIER DES PHASES ET AMPLITUDES)

TOMAWAC:
- FILE WITH COORDINATES OF SPECTRA TO IMPOSE
- FILE WITH COORDINATES OF SPECTRA TO WRITE
- IMPOSED SPECTRA FILE
- IMPOSED SPECTRA FILE FORMAT
- TAKING INTO ACCOUNT SOURCE TERMS ON IMPOSED BOUNDARIES
- TIME SHIFT OF IMPOSED SPECTRA FILE
- TIME UNIT OF IMPOSED SPECTRA FILE

Deleted keywords:
TELEMAC-3D:
- OPTION FOR THE DIFFUSION (OPTION POUR LA DIFFUSION), mnemo OPTDIF
- DIFFUSION STEP (ETAPE DE DIFFUSION), mnemo DIFFUS
- PROPAGATION STEP (ETAPE DE PROPAGATION), mnemo PROP

TOMAWAC:
- BINARY FILE 1 BINARY
- CURRENTS FILE BINARY
- DEFAULT EXECUTABLE
- DEFAULT PARALLEL EXECUTABLE
- DESCRIPTION OF LIBRARIES
- GEOMETRY FILE BINARY
- GLOBAL RESULT FILE BINARY
- PREVIOUS COMPUTATION FILE BINARY
- PUNCTUAL RESULTS FILE BINARY
- TIDAL WATER LEVEL FILE BINARY
- WINDS FILE BINARY

Documentation:
TELEMAC-3D:
- New theory guide for TELEMAC-3D. The previous release notes were removed
and shall be re-introduced in future versions to track version-specific changes.

Release V7P2R0 (31 Dec 2016)
===========================

Features
---------------------

- TELEMAC-2D: Add Spalart-Allmaras turbulence model.
- TelApy: Add the first structure for PYTHON API of TELEMAC.
- TELEMAC-3D: Add a new advection scheme (less diffusive scheme
  as in TELEMAC-2D).
- TELEMAC: Add possibility to prescribe space and time varying meteo
  conditions based on a file (ASCII ATMOSPHERIC DATA FILE and
  BINARY ATMOSPHERIC DATA FILE keywords).
- SISYPHE: Liquid boundaries file for bed load discharge.
- Replacing DredgeSim with Nestor.
- TELEMAC-2D: Add a new rainfall-runoff model. An example of use is given in
  the pluie test case.
- Automatic detection of Little/Big Endian for Serafin File
  (needs FORTRAN Gnu extension).
- TELEMAC-2D: Adding a deall_telemac2d subroutine that dallocates all that was
  allocated by point_telemac2d. Same thing for bief_all* and do on. This is
  mainly for API as in normal run the Fortran is cleaning on its own.
- TELEMAC-2D and 3D: new option for culvert modeling, change in the culvert parameters file.
- Adding NEWS file that contains the major modifications in the code.
- Integration of the MASCARET source code into the TELEMAC-MASCARET system
  (script mascaret.py to run code).
- TELEMAC-2D and 3D: possibility to read space-time varying meteo data from a
  binary file.
- TELEMAC-3D: possiblity to read space-time varying open boundary conditions
  from a binary file.

Addons
---------------------

- New version of ParaView plugin (SerafinReader) which allows to read Serafin
  file in Paraview.

Documentation
---------------------

- New developer guide in documentation/Misc/developer_guide.
- LaTeX documentation in folder documentation.