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#### Context
_Please provide informations on how to reproduce the bug:_
- [x] Branches impacted: current release and/or main
- [x] Reference configuration/test case (chosen or used as template) ~AMM ~gyre ~orca ~papa or engines involved ~ABL ~NST ~OFF ~TOP ~SAO ~SAS ~"SI³" ~SWE
- [x] Computing architecture: compiler, MPI & NetCDF libs (name and version)
- [x] Dependencies: ~AGRIF ~BFM ~CICE ~OASIS ~XIOS (with known branch and hash/revision/version), ...
- [ ] _Any other relevant information_
#### Analysis
_Please give your thoughts on the issue._
#### Fix
_Please share your proven solution or your recommendation on how to proceed._
---
_You can_
- :clipboard: _Copy code blocks_ (\`\`\`fortran ...\`\`\`) _or diff outputs_ (\`\`\`diff ...\`\`\`)
- :paperclip: _Include files_
- :link: _Add external links._
:warning: _Please remove all unnecessary lines in this description, like the one you are reading in italic, before creating the issue._ :warning:
#### Context
_Please provide informations on how to set the modelling environment_
- [ ] Reference configuration/test case (to add, chosen or used as template)
- [x] Modifications of versioned files: Fortran routines (`*.[Ffh]90`), namelists (`namelist\_*cfg`), outputs settings (`*.xml`), ...
- [ ] Additional dependencies
- [ ] New datasets
- [ ] _Any other relevant information_
#### Proposal
_Please share your ideas or your wishes about modelling improvements for the NEMO model._
_In particular, express if you are willing to contribute personally to the implementation of this feature in NEMO._
---
_You can_
- :clipboard: _Copy code blocks_ (\`\`\`fortran ...\`\`\`) _or diff outputs_ (\`\`\`diff ...\`\`\`)
- :paperclip: _Include files_
- :link: _Add external links._
:warning: _Please remove all unnecessary lines in this description, like the one you are reading in italic, before creating the issue._ :warning:
#### Development description
_Describe the goal and the methodology._
_Add reference documents or publications if relevant._
#### Code implementation
_Describe flow chart of the changes in the code._
_List the Fortran modules and subroutines to be created/edited/deleted._
_Detailed list of new variables to be defined (including namelists), give for each the chosen name and description wrt coding rules._
#### Documentation updates
_Using previous parts, define the main changes to be done in the ~doc (manuals, guide, web pages, ...)._
#### Tests
Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.
This part should contain the detailed results of ~SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test.
**Regular checks**
- [ ] Can this change be shown to produce expected impact (option activated)?
- [ ] Can this change be shown to have a null impact (option not activated)?
- [ ] Results of the required bit comparability tests been run: are there no differences when activating the development?
- [ ] If some differences appear, is reason for the change valid/understood?
- [ ] If some differences appear, is the impact as expected on model configurations?
- [ ] Is this change expected to preserve all diagnostics?
- [ ] If no, is reason for the change valid/understood?
- [ ] Are there significant changes in run time/memory?
#### Review
A successful review is needed to schedule the merge of this development into the future NEMO release during next Merge Party (usually in November).
**Assessments**
- [ ] Is the proposed methodology now implemented?
- [ ] Are the code changes in agreement with the flowchart defined at preview step?
- [ ] Are the code changes in agreement with list of routines and variables as proposed at preview step?
- [ ] If, not, are the discrepancies acceptable?
- [ ] Is the in-line documentation accurate and sufficient?
- [ ] Do the code changes comply with NEMO coding standards?
- [ ] Is the development documented with sufficient details for others to understand the impact of the change?
- [ ] Is the project ~doc (manual, guide, web, ...) now updated or completed following the proposed summary in preview section?
# compiler options for AA (using GCC compiler & OpenMPI)
#
# module use /home/ar0s/modules
# prgenv/gnu gcc/11.2.0 openmpi/4.1.1.1 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-impi
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
# All NETCDF and HDF paths are empty as they are automatically defined through environment
# variables by the load of modules
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
#
#
%NCDF_INC ${NETCDF4_INCLUDE}
#%NCDF_LIB ${NETCDF4_LIB} ${HDF5_LIB}
%NCDF_LIB ${NETCDF4_LIB} -L/usr/local/apps/hdf5-parallel/1.10.6/GNU/8.4/OMPI/4.1/lib -Wl,-rpath,/usr/local/apps/hdf5-parallel/1.10.6/GNU/8.4/OMPI/4.1/lib -lhdf5hl_fortran -lhdf5_hl_cpp -lhdf5_hl -lhdf5_fortran -lhdf5_cpp -lhdf5 -lm -lhdf5_hl -lhdf5
%XIOS_INC -I${XIOS_INC}
%XIOS_LIB -L${XIOS_LIB} -lxios
%OASIS_INC -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
%OASIS_LIB -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp -Dkey_nosignedzero
%FC mpif90 -c -cpp
#%FCFLAGS -fdefault-real-8 -O2 -ftree-vectorize -funroll-all-loops -ffree-line-length-none -Wno-missing-include-dirs
%FCFLAGS -fdefault-real-8 -O3 -ffree-line-length-none -Wno-missing-include-dirs -fallow-argument-mismatch
%FFLAGS %FCFLAGS
%LD mpif90
%LDFLAGS -lstdc++
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK gmake
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC mpicc
%CFLAGS -O0
# compiler options for AA (using INTEL compiler & INTEL MPI)
#
# module use /home/ar0s/modules
# module load prgenv/intel intel/2021.4.0 intel-mpi/2021.4.0 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-impi
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
# All NETCDF and HDF paths are empty as they are automatically defined through environment
# variables by the load of modules
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
#
#
%NCDF_INC ${NETCDF4_INCLUDE}
%NCDF_LIB ${NETCDF4_LIB} ${HDF5_LIB}
%XIOS_INC -I${XIOS_INC}
%XIOS_LIB -L${XIOS_LIB} -lxios -lstdc++
%OASIS_INC -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
%OASIS_LIB -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
%FC mpiifort -c -cpp
%FCFLAGS -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
%FFLAGS %FCFLAGS
%LD mpiifort
%LDFLAGS
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK gmake
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC mpiicc
%CFLAGS -O0
# compiler options for AA (using INTEL compiler & HPCX OpenMPI)
#
# module use /home/ar0s/modules
# module load prgenv/intel intel/2021.4.0 hpcx-openmpi/2.9.0 hdf5-parallel/1.10.6 netcdf4-parallel/4.7.4 xios/trunk/rev2320-xmpi
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
# All NETCDF and HDF paths are empty as they are automatically defined through environment
# variables by the load of modules
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
#
#
%NCDF_INC ${NETCDF4_INCLUDE}
%NCDF_LIB ${NETCDF4_LIB} ${HDF5_LIB}
%XIOS_INC -I${XIOS_INC}
%XIOS_LIB -L${XIOS_LIB} -lxios -lstdc++
%OASIS_INC -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
%OASIS_LIB -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
%FC mpifort -c -cpp
%FCFLAGS -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
%FFLAGS %FCFLAGS
%LD mpifort
%LDFLAGS
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK gmake
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC mpicc
%CFLAGS -O0
# compiler options for BELENOS/TARANIS (using INTEL compiler)
# compiler options for BELENOS/TARANIS (using INTEL compiler + INTEL MPI)
#
# INTEL_IMPI (XIOS-2.5)
# intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios-2.5_rev1903
# --------------------------------
# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
# --------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
#
# INTEL_IMPI (XIOS-TRUNK must be compiled)
# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
# ----------------------------------
# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
# ----------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
#
#
# NCDF_INC netcdf4 include file
......@@ -44,7 +50,7 @@
%NCDF_LIB -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
%XIOS_INC -I${XIOS_INC}
%XIOS_LIB -L${XIOS_LIB} -lxios -lstdc++
%OASIS_INC -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
%OASIS_INC -I${OASIS_DIR}/include
%OASIS_LIB -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
......
# compiler options for BELENOS/TARANIS (using INTEL compiler)
#
# INTEL_IMPI (XIOS-2.5)
# intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios-2.5_rev1903
# --------------------------------
# INTEL_IMPI (NEMO 4.0 + XIOS-2.5)
# --------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/2.5/rev1903
#
# INTEL_IMPI (XIOS-TRUNK must be compiled)
# gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2
# ----------------------------------
# INTEL_IMPI (NEMO 4.2 + XIOS-TRUNK)
# ----------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load gcc/9.2.0 intel/2018.5.274 intelmpi/2018.5.274 phdf5/1.8.18 netcdf_par/4.7.1_V2 xios/trunk/rev2134
#
#
# NCDF_INC netcdf4 include file
......@@ -44,7 +50,7 @@
%NCDF_LIB -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
%XIOS_INC -I${XIOS_INC}
%XIOS_LIB -L${XIOS_LIB} -lxios -lstdc++
%OASIS_INC -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
%OASIS_INC -I${OASIS_DIR}/include
%OASIS_LIB -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
......
# compiler options for BELENOS/TARANIS (using INTEL compiler + MVAPICH2 MPI)
#
# --------------------------------
# INTEL_MVAP (NEMO 4.0 + XIOS-2.5)
# --------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load intel/2018.5.274 mvapich2-2.3.5 hdf5-1.8.18-mvapich2 netcdf-4.7.1-mvapich2 xios/2.5/rev1903-mvapich2
#
# ----------------------------------
# INTEL_MVAP (NEMO 4.2 + XIOS-TRUNK)
# ----------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load gcc/9.2.0 intel/2018.5.274 mvapich2-2.3.5 hdf5-1.8.18-mvapich2 netcdf-4.7.1-mvapich2 xios/trink/rev2134-mvapich2
#
#
# NCDF_INC netcdf4 include file
# NCDF_LIB netcdf4 library
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
#
# FC Fortran compiler command
# FCFLAGS Fortran compiler flags
# FFLAGS Fortran 77 compiler flags
# LD linker
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
# FPPFLAGS pre-processing flags
# AR assembler
# ARFLAGS assembler flags
# MK make
# USER_INC complete list of include files
# USER_LIB complete list of libraries to pass to the linker
# CC C compiler used to compile conv for AGRIF
# CFLAGS compiler flags used with CC
#
# Note that:
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
# All NETCDF and HDF paths are empty as they are automatically defined through environment
# variables by the load of modules
#---------------------------------------------------------------------------------------------
#---------------------------------------------------------------------------------------------
#
#
%NCDF_INC -I${NETCDF_INC}
%NCDF_LIB -L${NETCDF_LIB} -lnetcdff -lnetcdf -L${PHDF5_LIB_DIR} -lhdf5_hl -lhdf5
%XIOS_INC -I${XIOS_INC}
%XIOS_LIB -L${XIOS_LIB} -lxios -lstdc++
%OASIS_INC -I${OASIS_DIR}/build/lib/mct -I${OASIS_DIR}/build/lib/psmile.MPI1
%OASIS_LIB -L${OASIS_DIR}/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp
%FC mpifort -c -cpp
%FCFLAGS -march=core-avx2 -i4 -r8 -O3 -fp-model strict -fno-alias -align array64byte
%FFLAGS %FCFLAGS
%LD mpifort
%LDFLAGS
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK gmake
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC mpicc
%CFLAGS -O0
# compiler options for BELENOS/TARANIS (using INTEL compiler)
# compiler options for BELENOS/TARANIS (using INTEL compiler + Open MPI)
#
# INTEL_OMPI (XIOS-2.5)
# intel/2018.5.274 openmpi/intel/4.0.2.2 hdf5-1.8.18-ompi netcdf-4.7.1-ompi_V2 xios-2.5_rev1903-ompi
# --------------------------------
# INTEL_OMPI (NEMO 4.0 + XIOS-2.5)
# --------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load intel/2018.5.274 openmpi/intel/4.0.2.2 hdf5-1.8.18-ompi netcdf-4.7.1-ompi_V2 xios/2.5/rev1903-ompi
#
# INTEL_MVAPICH2 (XIOS-2.5)
# intel/2018.5.274 mvapich2-2.3.5 hdf5-1.8.18-mvapich2 netcdf-4.7.1-mvapich2 xios-2.5_rev1903-mvapich2
# ----------------------------------
# INTEL_OMPI (NEMO 4.2 + XIOS-TRUNK)
# ----------------------------------
# module use /home/ext/mr/smer/samsong/modules
# module load gcc/9.2.0 intel/2018.5.274 openmpi/intel/4.0.2.2 hdf5-1.8.18-ompi netcdf-4.7.1-ompi_V2 xios/trunk/rev2134-ompi
#
#
# NCDF_INC netcdf4 include file
......
......@@ -35,7 +35,7 @@
%CPP cpp -Dkey_nosignedzero
%FC mpif90
%FCFLAGS -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none
%FCFLAGS -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none -fallow-argument-mismatch
%FFLAGS %FCFLAGS
%LD %FC
%LDFLAGS
......
......@@ -113,8 +113,8 @@
sn_trcsbc(7) = 'dust.orca.new' , -1 , 'dustsi' , .true. , .true. , 'yearly' , '' , '' , ''
sn_trcsbc(14) = 'dust.orca.new' , -1 , 'dustfer' , .true. , .true. , 'yearly' , '' , '' , ''
sn_trcsbc(23) = 'ndeposition.orca', -12 , 'ndep' , .false. , .true. , 'yearly' , '' , '' , ''
rn_trsfac(5) = 7.9258065e-02 ! ( 0.021 / 31. * 117 )
rn_trsfac(7) = 3.1316726e-01 ! ( 8.8 / 28.1 )
rn_trsfac(5) = 3.774194e-02 ! ( 1E-3 / 31. * 117 )
rn_trsfac(7) = 9.572954e-03 ! ( 8.8 / 28.1 )
rn_trsfac(14) = 6.2667860e-04 ! ( 0.035 / 55.85 )
rn_trsfac(23) = 5.2232143e-01 ! ( From kgN m-2 s-1 to molC l-1 ====> zfact = 7.3125/14 )
rn_sbc_time = 1. ! Time scaling factor for SBC and CBC data (seconds in a day)
......
......@@ -113,8 +113,8 @@
sn_trcsbc(7) = 'dust.orca.new' , -1 , 'dustsi' , .true. , .true. , 'yearly' , '' , '' , ''
sn_trcsbc(14) = 'dust.orca.new' , -1 , 'dustfer' , .true. , .true. , 'yearly' , '' , '' , ''
sn_trcsbc(23) = 'ndeposition.orca', -12 , 'ndep' , .false. , .true. , 'yearly' , '' , '' , ''
rn_trsfac(5) = 7.9258065e-02 ! ( 0.021 / 31. * 117 )
rn_trsfac(7) = 3.1316726e-01 ! ( 8.8 / 28.1 )
rn_trsfac(5) = 3.774194e-02 ! ( 1E-3 / 31. * 117 )
rn_trsfac(7) = 9.572954e-03 ! ( 8.8 / 28.1 )
rn_trsfac(14) = 6.2667860e-04 ! ( 0.035 / 55.85 )
rn_trsfac(23) = 5.2232143e-01 ! ( From kgN m-2 s-1 to molC l-1 ====> zfact = 7.3125/14 )
rn_sbc_time = 1. ! Time scaling factor for SBC and CBC data (seconds in a day)
......
......@@ -12,7 +12,7 @@
<domain domain_ref="grid_T" />
</grid>
<grid id="grid_T_2D_inner" >
<domain domain_ref="grid_T_inner" />
<domain domain_ref="grid_T_inner" name="grid_T" />
</grid>
<!-- -->
<grid id="grid_T_ncatice" >
......@@ -20,7 +20,7 @@
<axis axis_ref="ncatice" />
</grid>
<grid id="grid_T_ncatice_inner" >
<domain domain_ref="grid_T_inner" />
<domain domain_ref="grid_T_inner" name="grid_T" />
<axis axis_ref="ncatice" />
</grid>
<!-- -->
......@@ -29,7 +29,7 @@
<axis axis_ref="deptht" />
</grid>
<grid id="grid_T_3D_inner" >
<domain domain_ref="grid_T_inner" />
<domain domain_ref="grid_T_inner" name="grid_T" />
<axis axis_ref="deptht" />
</grid>
<!-- -->
......@@ -38,7 +38,7 @@
<axis axis_ref="profsed" />
</grid>
<grid id="grid_T_3DS_inner" >
<domain domain_ref="grid_T_inner" />
<domain domain_ref="grid_T_inner" name="grid_T" />
<axis axis_ref="profsed" />
</grid>
<!-- -->
......@@ -46,7 +46,7 @@
<domain domain_ref="grid_U" />
</grid>
<grid id="grid_U_2D_inner" >
<domain domain_ref="grid_U_inner" />
<domain domain_ref="grid_U_inner" name="grid_U" />
</grid>
<!-- -->
<grid id="grid_U_3D" >
......@@ -54,7 +54,7 @@
<axis axis_ref="depthu" />
</grid>
<grid id="grid_U_3D_inner" >
<domain domain_ref="grid_U_inner" />
<domain domain_ref="grid_U_inner" name="grid_U" />
<axis axis_ref="depthu" />
</grid>
<!-- -->
......@@ -62,7 +62,7 @@
<domain domain_ref="grid_V" />
</grid>
<grid id="grid_V_2D_inner" >
<domain domain_ref="grid_V_inner" />
<domain domain_ref="grid_V_inner" name="grid_V" />
</grid>
<!-- -->
<grid id="grid_V_3D" >
......@@ -70,7 +70,7 @@
<axis axis_ref="depthv" />
</grid>
<grid id="grid_V_3D_inner" >
<domain domain_ref="grid_V_inner" />
<domain domain_ref="grid_V_inner" name="grid_V" />
<axis axis_ref="depthv" />
</grid>
<!-- -->
......@@ -78,7 +78,7 @@
<domain domain_ref="grid_W" />
</grid>
<grid id="grid_W_2D_inner" >
<domain domain_ref="grid_W_inner" />
<domain domain_ref="grid_W_inner" name="grid_W" />
</grid>
<!-- -->
<grid id="grid_W_3D" >
......@@ -86,7 +86,7 @@
<axis axis_ref="depthw" />
</grid>
<grid id="grid_W_3D_inner" >
<domain domain_ref="grid_W_inner" />
<domain domain_ref="grid_W_inner" name="grid_W" />
<axis axis_ref="depthw" />
</grid>
<!-- -->
......@@ -94,7 +94,7 @@
<domain domain_ref="grid_F" />
</grid>
<grid id="grid_F_2D_inner" >
<domain domain_ref="grid_F_inner" />
<domain domain_ref="grid_F_inner" name="grid_F" />
</grid>
<!-- -->
<grid id="grid_F_3D" >
......@@ -102,7 +102,7 @@
<axis axis_ref="depthf" />
</grid>
<grid id="grid_F_3D_inner" >
<domain domain_ref="grid_F_inner" />
<domain domain_ref="grid_F_inner" name="grid_F" />
<axis axis_ref="depthf" />
</grid>
<!-- -->
......
¤ Missing namelist groups in NEMO manual
namage namagrif namalb namc14_fcg namc14_sbc namc14_typ namc1d namc1d_dyndmp namc1d_uvd namcfc namcrs namdia namdrg namdrg_bot namdrg_top namdta_dyn namdyn namdyn_rdgrft namdyn_rhg namforcing namhsb namini namitd namlobdet namlobdom namlobnut namlobopt namlobphy namlobrat namlobsed namlobzoo nammpp namp4zlim namp4zmes namp4zmort namp4zprod namp4zzoo namp5zlim namp5zmes namp5zmort namp5zprod namp5zquota namp5zzoo nampar nampisatm nampisbio nampiscal nampisdmp nampisext nampisfer nampisice nampislig nampismass nampismod nampisopt nampispoc nampisrem nampissbc namsbc_blk namsbc_iif namthd namthd_da namthd_do namthd_pnd namthd_sal namthd_zdf namtra_eiv namtra_mle namtrc namtrc_adv namtrc_bc namtrc_bdy namtrc_dmp namtrc_dta namtrc_ice namtrc_ldf namtrc_rad namtrc_run namtrc_snk namtrc_trd nam_vvl namzdf_iwm
¤ Vanished index entries in NEMO manual (\{hf,jp,key,mdl,ngn,nlst,np,rou}{...})
chap_DYN.tex: key{dynspg\_exp} key{dynspg\_flt} key{dynspg\_ts} key{trddyn} key{trdvor} key{vvl} mdl{dynspg\_flt} mdl{zpsdhe} nlst{namsplit} np{ln\_bt\_nn\_auto} np{ln\_dynhpg\_djc} np{ln\_dynhpg\_imp} np{ln\_dynhpg\_isf} np{ln\_dynhpg\_prj} np{ln\_dynhpg\_sco} np{ln\_dynhpg\_vec} np{ln\_dynhpg\_zco} np{ln\_dynhpg\_zps} np{ln\_dynldf\_bilap} np{ln\_dynvor\_con} np{ln\_dynzad\_zts} np{ln\_traadv\_tvd\_zts} np{ln\_wd\_dl\_ramp} np{ln\_zdfexp} np{nn\_atfp} np{nn\_dynhpg\_rst} np{nn\_ice\_embd} np{nn\_zdfexp}
introduction.tex:
chap_model_basics_zstar.tex: key{dynspg\_exp} key{dynspg\_flt} key{dynspg\_ts} key{vvl} mdl{dynspg\_flt} np{rdtbt} np{rnu}
chap_DIA.tex: key{diaar5} key{diadct} key{diaharm} key{diahth} key{diainstant} key{floats} key{xios} key{netcdf4} key{trdmld\_trc} key{trdtrc} key{vvl} ngn{namdia\_harm} np{init\_float\_ariane} rou{iom\_put} np{jpnflnewflo} np{nb\_ana} np{nit000} np{nitend} np{nn\_debug} np{nn\_diacfl} np{tname} rou{iom\_rstput}
annex_E.tex: key{traldf\_eiv}
chap_TRA.tex: jp{lk\_vvl} key{trabbl} key{traTTT} key{zdfddm} mdl{traldf\_lap} ngn{namtra\_bbc} np{ln\_flxqsr} np{ln\_sco} np{ln\_traadv\_NONE} np{ln\_traldf} np{ln\_traldf\_grif} np{ln\_traldf\_NONE} np{ln\_tsd\_tradmp} np{ln\_useCT} np{ln\_zco} np{ln\_zdfexp} np{ln\_zps} np{nn\_chdta} np{nn\_eos} np{nn\_fct\_zts} np{nn\_geoflx\_cst} np{nn\_zdfexp} rou{traldf\_blp} rou{traldf\_lap}
chap_DIU.tex:
chap_ASM.tex: key{asminc} ngn{namasm}
chap_ZDF.tex: key{dynspg\_exp} key{dynspg\_flt} key{dynspg\_ts} key{trabbl} key{vvl} key{zdf} key{zdfcst} key{zdfddm} key{zdfgls} key{zdfosm} key{zdfric} key{zdftke} key{zdftmx} key{zdftmx\_new} mdl{dynbfr} mdl{dynzdf\_imp} mdl{zdfbfr} mdl{zdfini} mdl{zdfkpp} ngn{namzdf\_ddm} ngn{namzdf\_tmx} ngn{namzdf\_tmx\_new} nlst{nambfr} nlst{namzdf_ddm} nlst{namzdf_tmx} nlst{namzdf_tmx_new} np{ln\_bfr2d} np{ln\_bfrimp} np{ln\_crban} np{ln\_tmx\_itf} np{ln\_tranpc} np{ln\_zdfexp} np{ln\_zdftmx\_itf} np{nn\_botfr} np{nn\_clo} np{nn\_ediff} np{nn\_ediss} np{nn\_tkebc\_bot} np{nn\_tkebc\_surf} np{rn\_avevd} np{rn\_bfeb2} np{rn\_bfri1} np{rn\_bfri2} np{rn\_bfri2\_max} np{rn\_bfrien} np{rn\_bfrz0} np{rn\_htmx} np{rn\_me} np{rn\_n2min} np{rn\_tfe} np{rn\_tfe\_itf} np{rn\_tfri2} np{rn\_tfri2\_max} np{rn\_tfrz0} rou{zdf\_bfr}
chap_OBS.tex:
chap_misc.tex: key{nosignedzero} np{iom\_get} np{jpjdta} np{jpjglo} np{nn\_bench} np{nn\_bit\_cmp} np{open\_ocean\_jstart}
chap_LDF.tex: hf{dynldf\_cNd} hf{ldfdyn\_substitute} hf{ldftra\_substitute} hf{traldf\_c1d} hf{traldf\_cNd} key{dynldf\_c1d} key{dynldf\_c2d} key{dynldf\_c3d} key{traldf\_c1d} key{traldf\_c2d} key{traldf\_c3d} key{traldf\_cNd} key{traldf\_eiv} mdl{ldfdyn\_c2d} mdl{ldfeiv} mdl{traadv\_eiv} np{ln\_dynldf\_bilap} np{ln\_sco} np{nn\_eos} np{rn\_aeih\_0} np{rn\_aeiv} np{rn\_aeiv\_0} np{rn\_ahm0} np{rn\_ahmb0} np{rn\_aht0} np{rn\_ahtb0} np{traldf\_grif} np{traldf\_grif\_iso} rou{ldf\_dyn\_c2d\_orca} rou{ldfslp\_init}
chap_LBC.tex: jp{jpreci} key{mpi\_off} np{jpiglo} np{jpindt} np{jpinft} np{jpjglo} np{jpjnob} np{nbdysegn} np{nn\_bdy\_jpk} np{nn\_msh} np{nn\_tra}
chap_DOM.tex: ngn{namzgr} ngn{namzgr\_sco} nlst{namzgr} nlst{namzgr_sco} np{jpiglo} np{jpjglo} np{jpkglo} np{ln\_sco} np{ln\_sigcrit} np{ln\_s\_SF12} np{ln\_s\_SH94} np{ln\_tsd\_ini} np{ln\_zco} np{ln\_zps} np{nn\_bathy} np{nn\_msh} np{ppa0} np{ppa1} np{ppacr} np{ppdzmin} np{pphmax} np{ppkth} np{ppsur} np{rn\_alpha} np{rn\_bb} np{rn\_e3zps\_min} np{rn\_e3zps\_rat} np{rn\_hc} np{rn\_rmax} np{rn\_sbot\_max} np{rn\_sbot\_min} np{rn\_theta} np{rn\_zb\_a} np{rn\_zb\_b} np{rn\_zs} rou{istate\_t\_s}
chap_conservation.tex: key{\_}
annex_iso.tex: key{trabbl} key{traldf\_eiv} np{ln\_traldf\_eiv} np{ln\_traldf\_gdia}
chap_time_domain.tex: np{ln\_zdfexp} np{nn\_dynhpg\_rst} np{nn\_zdfexp}
annex_C.tex:
chap_CONFIG.tex: key{agrif} key{c1d} key{dynspg\_ts} key{orca\_r12} key{orca\_r8} key{vvl} key{zdfgls} ngn{namusr\_def} np{jpiglo} np{jpizoom} np{jpjglo} np{jpjzoom} np{ln\_bench} np{nn\_GYRE} np{ORCA\_index}
chap_SBC.tex: key{cice} key{coupled} key{cpl\_carbon\_cycle} key{lim3} key{nemocice\_decomp} key{oasis3} key{pisces} key{top} key{vvl} mdl{sbcana} mdl{sbc\_ana\_gyre} mdl{sbcsas} ngn{namsbc\_ana} ngn{namsbc\_clio} ngn{namsbc\_core} nlst{namsbc_ana} nlst{namsbc_clio} nlst{namsbc_core} np{clim} np{ln\_ana} np{ln\_blk\_clio} np{ln\_blk\_core} np{ln\_clio} np{ln\_core} np{ln\_rnf\_temp} np{nn\_nit000} np{nn\_tau000} np{nn\_test\_box} np{nz\_rnf} np{rn\_emp0} np{rn\_fiscpl} np{rn\_qns0} np{rn\_qsr0} np{rn\_utau0} np{rn\_vtau0}
chap_STO.tex:
¤ Namelist parameters unfollowing naming conventions (^[cdlnr]n_* or uppercase somewhere)
nam_asminc: nitbkg nitdin nitiaustr nitiaufin niaufn salfixmin
nambbc: sn_qgh
nambdy: nb_bdy nb_jpk_bdy ctypebdy nbdyind nbdybeg nbdyend
nambdy_dta: bn_ssh bn_u2d bn_v2d bn_u3d bn_v3d bn_tem bn_sal
nambdy_tide: filtide
namberg: rn_LoW_ratio sn_icb
namc14_fcg: cfileco2 cfilec14 tyrc14_beg
namc14_sbc: xkwind xdicsur
namc14_typ: kc14typ rc14at pco2at rc14init
namc1d_uvd: sn_ucur sn_vcur
namcfc: ndate_beg nyear_res clname
namdia: iiceprt jiceprt
nam_diaharm: nit000_han nitend_han nstep_han tname(1) tname(2)
namdrg: ln_drg_OFF
namdrg_bot: rn_Cd0 rn_Uc0 rn_Cdmax
namdrg_top: rn_Cd0 rn_Uc0 rn_Cdmax
namdta_dyn: sn_tem sn_sal sn_mld sn_emp sn_fmf sn_ice sn_qsr sn_wnd sn_uwd sn_vwd sn_wwd sn_avt sn_ubl sn_vbl
namdyn: ln_dynALL ln_dynRHGADV ln_dynADV1D ln_dynADV2D ln_landfast_L16
namdyn_adv: ln_dynadv_OFF
namdyn_ldf: ln_dynldf_OFF rn_Uv rn_Lv
namdyn_rdgrft: ln_str_H79
namdyn_rhg: ln_rhg_EVP ln_aEVP
namdyn_vor: ln_dynvor_enT ln_dynvor_eeT
namflo: jpnfl jpnnewflo
namforcing: nice_jules
namini: sn_hti sn_hts sn_ati sn_tsu sn_tmi sn_smi
namlobdet: taudn fdetlab
namlobdom: taudomn
namlobnut: akno3 aknh4 taunn psinut
namlobopt: xkg0 xkr0 xkgp xkrp xlg xlr rpig
namlobphy: tmumax rgamma fphylab tmminp aki
namlobrat: rcchl redf reddom
namlobsed: sedlam sedlostpoc vsed xhr
namlobzoo: rppz taus aks rpnaz rdnaz tauzn fzoolab fdbod tmminz
nammpp: jpni jpnj
namp4zlim: concnno3 concdno3 concnnh4 concdnh4 concnfer concdfer concbfe concbnh4 concbno3 xsizedia xsizephy xsizern xsizerd xksi1 xksi2 xkdoc qnfelim qdfelim caco3r oxymin
namp4zmes: part2 grazrat2 resrat2 mzrat2 xpref2d xpref2n xpref2z xpref2c xthresh2zoo xthresh2dia xthresh2phy xthresh2poc xthresh2 xkgraz2 epsher2 epsher2min sigma2 unass2 grazflux
namp4zmort: wchl wchld wchldm mprat mprat2
namp4zprod: pislopen pisloped xadap excretn excretd bresp chlcnm chlcdm chlcmin fecnm fecdm grosip
namp4zzoo: part grazrat resrat mzrat xprefc xprefn xprefd xthreshdia xthreshphy xthreshpoc xthresh xkgraz epsher epshermin sigma1 unass
namp5zlim: concnno3 concpno3 concdno3 concnnh4 concpnh4 concdnh4 concnpo4 concppo4 concdpo4 concnfer concpfer concdfer concbfe concbnh4 concbno3 concbpo4 xsizedia xsizephy xsizepic xsizern xsizerp xsizerd xksi1 xksi2 xkdoc caco3r oxymin
namp5zmes: part2 grazrat2 bmetexc2 resrat2 mzrat2 xpref2d xpref2p xpref2z xpref2m xpref2c xthresh2zoo xthresh2dia xthresh2phy xthresh2mes xthresh2poc xthresh2 xkgraz2 epsher2 epsher2min ssigma2 srespir2 unass2c unass2n unass2p grazflux
namp5zmort: wchln wchlp wchld wchldm mpratn mpratp mprat2
namp5zprod: pislopen pislopep pisloped excretn excretp excretd xadap bresp thetannm thetanpm thetandm chlcmin grosip
namp5zquota: qfnopt qfpopt qfdopt qnnmin qnnmax qpnmin qpnmax qnpmin qnpmax qppmin qppmax qndmin qndmax qpdmin qpdmax qfnmax qfpmax qfdmax
namp5zzoo: part grazrat bmetexc resrat mzrat xprefc xprefn xprefp xprefd xprefz xthreshdia xthreshphy xthreshpic xthreshzoo xthreshpoc xthresh xkgraz epsher epshermin ssigma srespir unassc unassn unassp
nampar: jpl nlay_i nlay_s
nampisatm: sn_patm sn_atmco2
nampisbio: nrdttrc wsbio xkmort ferat3 wsbio2 wsbio2max wsbio2scale ldocp ldocz lthet no3rat3 po4rat3
nampiscal: kdca nca
nampisext: atcco2 clname
nampisfer: xlam1 xlamdust ligand kfep
nampisice: sn_tri_dic sn_tri_doc sn_tri_tal sn_tri_oxy sn_tri_cal sn_tri_po4 sn_tri_poc sn_tri_goc sn_tri_bfe sn_tri_num sn_tri_sil sn_tri_dsi sn_tri_gsi sn_tri_phy sn_tri_dia sn_tri_zoo sn_tri_mes sn_tri_fer sn_tri_sfe sn_tri_dfe sn_tri_nfe sn_tri_nch sn_tri_dch sn_tri_no3 sn_tri_nh4
nampislig: rlgw rlig prlgw rlgs
nampisopt: sn_par parlux
nampispoc: xremip jcpoc rshape xremipc xremipn xremipp
nampisrem: xremik nitrif xsirem xsiremlab xsilab feratb xkferb xremikc xremikn xremikp
nampissbc: sn_dust sn_solub sn_riverdic sn_riverdoc sn_riverdin sn_riverdon sn_riverdip sn_riverdop sn_riverdsi sn_ndepo sn_ironsed sn_hydrofe sedfeinput distcoast dustsolub mfrac wdust icefeinput nitrfix diazolight concfediaz hratio lgw_rath
namsbc_apr: sn_apr
namsbc_blk: ln_NCAR ln_COARE_3p0 ln_COARE_3p5 ln_ECMWF ln_Cd_L12 ln_Cd_L15 sn_wndi sn_wndj sn_qsr sn_qlw sn_tair sn_humi sn_prec sn_snow sn_slp sn_tdif
namsbc_cpl: sn_snd_temp sn_snd_alb sn_snd_thick sn_snd_crt sn_snd_co2 sn_snd_crtw sn_snd_ifrac sn_snd_wlev sn_snd_cond sn_snd_thick1 sn_snd_mpnd sn_snd_sstfrz sn_snd_ttilyr sn_rcv_w10m sn_rcv_taumod sn_rcv_tau sn_rcv_dqnsdt sn_rcv_qsr sn_rcv_qns sn_rcv_emp sn_rcv_rnf sn_rcv_cal sn_rcv_co2 sn_rcv_hsig sn_rcv_iceflx sn_rcv_mslp sn_rcv_phioc sn_rcv_sdrfx sn_rcv_sdrfy sn_rcv_wper sn_rcv_wnum sn_rcv_wstrf sn_rcv_wdrag sn_rcv_ts_ice sn_rcv_isf sn_rcv_icb sn_rcv_tauwoc sn_rcv_tauw sn_rcv_wdrag
namsbc_flx: sn_utau sn_vtau sn_qtot sn_qsr sn_emp
namsbc_iif: sn_ice
namsbc_isf: sn_fwfisf sn_rnfisf sn_depmax_isf sn_depmin_isf sn_Leff_isf
namsbc_rnf: sn_rnf sn_cnf sn_s_rnf sn_t_rnf sn_dep_rnf
namsbc_sas: l_sasread sn_usp sn_vsp sn_tem sn_sal sn_ssh sn_e3t sn_frq
namsbc_ssr: sn_sst sn_sss
namsbc_wave: sn_cdg sn_usd sn_vsd sn_hsw sn_wmp sn_wfr sn_wnum sn_tauwoc sn_tauwx sn_tauwy
namthd: ln_icedH ln_icedA ln_icedO ln_icedS
namthd_do: rn_Cfraz
namthd_pnd: ln_pnd_H12 ln_pnd_CST
namthd_zdf: ln_zdf_BL99 ln_cndi_U64 ln_cndi_P07
nam_tide: rdttideramp clname(1)
namtra_adv: ln_traadv_OFF
namtra_eiv: rn_Ue rn_Le
namtra_ldf: ln_traldf_OFF rn_Ud rn_Ld
namtra_qsr: sn_chl
namtrc: jp_bgc jp_dia3d jp_dia2d
namtrc_adv: ln_trcadv_OFF
namtrc_dta: sn_trcdta(1)
namtrc_ldf: ln_trcldf_OFF
namtrc_snk: nitermax
namtrd: ln_KE_trd ln_PE_trd
namtsd: sn_tem sn_sal
namzdf: ln_zad_Aimp
**************************
Building the documentation
**************************
.. todo::
:file:`latex` : LaTeX sources and Latexmk configuration to build reference manuals with :file:`manual_build.sh`
:file:`namelists`: Namelist blocks included in the documentation
:file:`rst` : |RST man|_ sources and Sphinx configuration to build this guide hereby with :file:`guide_build.sh`
.. |RST man| replace:: reStructuredText (rst)
.. warning::
Mention `svnignore` hidden file
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