source: utils/tools/SIREN/src/docsrc/5_changeLog.md @ 13369

# Change log

@tableofcontents

# Release 2020-07-30 {#rev_2020-07-30}
# Bug fix
- M mpp.f90 :
   - look for array index of proc id, only if proc id contains in array
- M iom_cdf.f90 :
   - use 2D start and count array (for each variable), if present as argument
- M create_restart.f90 :
   - do not check domain validity, if source and target coordinates are the same

# Release 2020-07-27 {#rev_2020-07-27}
# Bug fix
use right indices to write variable on netcdf file
- M src/iom.f90 :
   - use 2D start and count arrays
- M src/iom_mpp.f90 :
   - compute start and count arrays (2D, for each variable)
- M src/mpp.f90 :
   - call dim_reorder for each proc file
   - add variable's dimension argument to set up mpp structure
- M src/iom_cdf.f90 :
   - use 2D start and count array (for each variable)
- M src/file.f90 :
   - keep file order indices, when adding dimension

# Release 2019-12-03 {#rev_2019-12-03}
## New features
- M Siren/src/iom_cdf.f90 :
   - write netcdf file as netcdf4

# Release 2019-11-05 {#rev_2019-11-05}
## New features
- M Siren/src/function.f90
- M src/create_bathy.f90 :
   - add help and version optional arguments
   - update header for usage
- M src/create_boundary.F90 :
   - add help and version optional arguments
   - update header for usage
- M src/create_coord.f90 :
   - add help and version optional arguments
   - update header for usage
- M src/create_layout.f90 :
   - add help and version optional arguments
   - update header for usage
- M src/create_meshmask.f90 :
   - add help and version optional arguments
   - update header for usage
- M src/create_restart.f90 :
   - add help and version optional arguments
   - update header for usage
- M src/merge_bathy.f90 :
   - add help and version optional arguments
   - update header for usage
- M src/function.f90 :
   - add help and version functions
- M src/global.f90 :
   - add parameter for version, author, and date
   - set SVN keyword Revision, Author, and Date

# Release 2019-10-18 {#rev_2019-10-18}
## New Features
- A templates/README
- A templates/create_templates.py :
   - script to create template of namelist from Siren sources
## Changes
- M templates/addline.nam :
   - update template of namelist (with default value)
- M templates/create_bathy.nam :
   - update template of namelist (with default value)
- M templates/create_boundary.nam :
   - update template of namelist (with default value)
- M templates/create_coord.nam :
   - update template of namelist (with default value)
- M templates/create_restart.nam :
   - update template of namelist (with default value)
- M templates/merge_bathy.nam :
   - update template of namelist (with default value)

# Release 2019-08-12 {#rev_2019-08-12}
## Changes
- src/create_bathy.f90 :
   - use periodicity read from namelist, and store in multi structure
- src/create_boundary.F90 :
   - use periodicity read from namelist, and store in multi structure
- src/create_restart.f90 :
   - use periodicity read from namelist, and store in multi structure
- src/mpp.f90 :
   - change print format
- src/multi.f90 :
   - use periodicity read from namelist, and store in multi structure
- templates/addline.nam :
   - rename sub namelist namcrs to namsrc
- templates/create_bathy.nam :
   - rename sub namelist namcrs to namsrc
   - rename sub namelist namfin to namtgt
- templates/create_boundary.nam :
   - rename sub namelist namcrs to namsrc
- rename sub namelist namfin to namtgt
- templates/create_coord.nam :
   - rename sub namelist namcrs to namsrc
- templates/create_restart.nam :
   - rename sub namelist namcrs to namsrc
   - rename sub namelist namfin to namtgt
## Bug fixes
- src/create_layout.f90 :
   - add missing variable in logger namelist
- src/multi.f90 :
   - rewrite function to subroutine
   - output filename string contains only filename (no more periodicity if given)

# Release 2019-05-21 {#rev_2019-05-21}
## New Features
- src/date.f90 :
   - add date_time subroutine
## Changes
- src/create_restart.f90 :
   - force number of proc to one by default
   - create and clean file structure to avoid memory leaks
- src/file.f90 :
   - add option to check dimension axis but not length
- src/grid.f90 :
   - do not use latitude variable to get pivot
   - read only grid boundaries to handle huge file
   - define as module variable im_max_overlap
- src/iom.f90 :
   - permit to write header and variable independantly
   - split iom_write_file into write_header and write_var
- src/iom_cdf.f90 :
   - permit to write header and variable independantly
   - split iom_cdf_write_file into write_header and write_var
   - add dimension structure as optional argument
   - do not check variable dimension if dimension forced
- src/iom_dom.f90 :
   - copy variable struct without array of value, then read array of value
- src/iom_mpp.f90 :
   - handle use of domain decomposition for monoproc file
- src/iom_rstdimg.f90 :
   - handle use of domain decomposition for monoproc file
   - split iom_rstdimg_write_file into write_header and write_var
- src/merge_bathy.f90 :
   - create and clean file structure to avoid memory leaks
- src/mpp.f90 :
   - cosmetic change
   - use mpp decomposition for writing netcdf
   - force to use domain decomposition to enhance read of monoproc file
   - add mpp__add_proc_arr
   - handle use of domain decomposition for monoproc file
- src/variable.f90 :
   - permit to copy variable structure without value
## Bug fixes
- src/math.f90 :
   - use the correct loop index to look for element bigger than pivot point
- src/multi.f90 :
   - compare each elt of cl_tabfile to cl_file

# Release 2019-05-15 {#rev_2019-05-15}
## New Features
- src/addline_deg.f9 :
   - new program to add line to all variable of the input file
- src/create_layout.f90 :
   - new program to create/compute the domain layout
- src/create_meshmask.f90 :
   - new program to create meshmask or domain.cfg
- src/grid_hgr.f90 :
   - new module needed to create meshmask
- src/grid_zgr.f90 :
   - new module needed to create meshmask
- src/lbc.f90 :
   - new module needed to create meshmask
- src/create_bathy.f90 :
   - optionaly, add random value to a flat bathymetry
- src/global.f90 :
   - add svn keyword properties
- src/math.f90 :
   - add function math_ortho
   - add function math_euclid
- src/multi.f90 :
   - add function multi__get_perio
- src/variable.f90 :
   - add function var_chg_name to rename variable
   - add output name to variable structure
## Changes
- src/create_bathy.f90 :
   - add url path to global attributes of output file(s)
   - create and clean file structure to avoid memory leaks
   - check dimension of matrix for 'handmade' bathymetry
   - check name and standard name for longitude and latitude
   - rewrite header (doc)
   - rename sub namelist namcrs to namsrc
   - rename sub namelist namfin to namtgt
   - change NEMO path
- src/create_boundary.F90 :
   - add url path to global attributes of output file(s)
   - explain how to fill Lateral Boundary Condition in NEMO namelist
   - create and clean file structure to avoid memory leaks
   - rewrite header (doc)
   - rename sub namelist namcrs to namsrc
   - rename sub namelist namfin to namtgt
   - change NEMO path
- src/create_coord.f90 :
   - add url path to global attributes of output file(s)
   - create and clean file structure to avoid memory leaks
   - rewrite header (doc)
   - rename sub namelist namcrs to namsrc
- src/create_restart.f90 :
   - add url path to global attributes of output file(s)
   - check name and standard name for longitude and latitude
   - rewrite header (doc)
   - rename sub namelist namcrs to namsrc
   - rename sub namelist namfin to namtgt
   - change NEMO path
- src/global.f90 :
   - define svn url
- src/merge_bathy.f90 :
   - add url path to global attributes of output file(s)
   - rewrite header (doc)
   - rename sub namelist namcrs to namsrc
   - rename sub namelist namfin to namtgt
   - change NEMO path
- src/create_meshmask.f90 :
   - change NEMO path
- src/mpp.f90 :
   - copy file periodicity to mpp structure
   - clean file, variable, and attributes structures
   - deallocate file structure whatever happens
   - do not split variable on domain decomposition, if only one procesor
   - nullify array in layout structure
   - nullify file structure inside mpp structure
- src/attribute.f90 :
   - nullify array inside attribute structure
- src/boundary.f90 :
   - nullify segment structure inside boundary structure
- src/date.f90 :
   - check time units CF convention, raise error if not
- src/dimension.f90 :
   - do not reshape array already order
- src/file.f90 :
   - clean variable, attributes, and dimension structures
   - nullify variable, attributes structures inside file structure
   - netcdf4 files identify as netcdf file
- src/function.f90 :
   - permit sign as first character
- src/grid.f90 :
   - do not use silicalim, or silicamax to get pivot point
   - check name and standard name for latitude
- src/iom_cdf.f90 :
   - clean variable, attributes, and dimension structures
   - read array in netcdf file, level by level, and time step by time step
   - apply scale factor and offset, level by level, and time step by time step
   - check attribute array is allocated, before use it
- src/iom_rstdimg.f90 :
   - clean dimension structure
- src/multi.f90 :
   - create and clean file structure to avoid memory leaks
   - fill value read from array of variable structure
   - nullify mpp structure in multi file structure
   - deallocate mpp structure whatever happens
   - print periodicity
- src/phycst.f90 :
   - half reduce epsilon value
- src/variable.f90 :
   - use scalar instead of array, as transitional variable
   - nullify attributes structure inside variable strcuture
   - decompose array conversion on each dimension
   - decompose array copy on each dimension
   - deallocate attribute strucure whatever happens
   - clean attribute strucure
   - nullify array inside variable structure
   - write fill value on array, level by level
- src/docsrc/main.dox :
   - add create_meshmask to SIREN tools list
   - add create_layout to SIREN tools list
- src/docsrc/1_install.md :
   - change NEMO path
- src/docsrc/2_quickstart.md :
   - change link to SIREN inputs
   - add description of create_meshmask
   - add description of create_layout
## Bug fixes
- src/function.f90 :
   - permit negative exposant
- src/iom_cdf.f90 :
   - use dimid to look for the index of the dimension, and not as dimension index
- src/mpp.f90 :
   - netcdf proc indices from zero to N-1
- src/variable.f90 :
   - check if tg_varextra is allocated before clean it
   - add case for units in hours
   - read number of element for each dummy array in configuration file
- src/attributes.f90 :
   - read and use number of element for each dummy array in configuration file
- src/multi.f90 :
   - specify format output
- src/dimension.f90 :
   - read number of element for each dimension allowed in configuration file
   - read number of element for each dummy array in configuration file

# Release 2016-11-16 {#rev_2016-11-16}
## New Features
- create_meshmask.f90 program to create meshmask from coordinates and bathymetry files.
- create_meshmask.f90 allows to write domain_cfg file.
- merge_bathy.f90:
   - allow to choose the number of boundary point with coarse grid value.
- dimension.f90:
   - dimension allowed read in configuration file.
- variable.f90:
   - allow to add scalar value.
- create_meshmask.f90:
   - choose vertical scale factors (e3.=dk[depth] or old definition).
## Changes
- create_coord.f90:
   - allow to define sub domain with coarse grid indices or coordinates.
- grid.f90:
   -grid__get_closest_str:
   - add function to get closest grid point using coarse grid coordinates strucutre.
- iom_cdf.f90:
   -iom_cdf__get_info:
   - define cdf4 as cdf.
- variable.f90:
   - add subroutine to clean global array of extra information, and define logical for variable to be used.
- create_coord.f90:
   - dimension to be used select from configuration file.
- create_bathy.f90:
   - dimension to be used select from configuration file.
- merge_bathy.f90:
   - dimension to be used select from configuration file.
- create_boundary.f90:
   - dimension to be used select from configuration file.
- create_restart.f90:
   - dimension to be used select from configuration file.
## Bug fixes
- boundary.f90:
   -boundary_check:
   - take into account that boundaries are compute on T point, but expressed on U,V point.
- grid.f90:
   -grid__get_closest_str:
   - use max of zero and east-west overlap instead of east-west overlap.
- mpp.f90:
   - compare index to td_lay number of proc instead of td_mpp (bug fix) .
- iom_cdf.f90 :
   - check if attribute cl_value is not bug (in read file)

# Release 2016-07-01 {#rev_2016-07-01}

## Changes
## New Features
## Bug fixes
- correct check of boundary indices

# Initial Release 2016-04-11 {#rev_2016-04-11}
   <HR>
   <b>
   - @ref index
   - @ref md_src_docsrc_1_install
   - @ref md_src_docsrc_2_quickstart
   - @ref md_src_docsrc_3_support_bug
   - @ref md_src_docsrc_4_codingRules
   - @ref todo
   </b>