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arch/arch-linux_pgf90.fcm
View file @ f6cac17d
......@@ -21,7 +21,7 @@
%FFLAGS %FCFLAGS
%LD pgf90
%LDFLAGS
%FPPFLAGS -P -C -traditional
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS -rs
%MK gmake
......
arch/arch-osx_gfortran.fcm
View file @ f6cac17d
......@@ -35,7 +35,8 @@
%CPP cpp -Dkey_nosignedzero
%FC mpif90
%FCFLAGS -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none
%PROD_FCFLAGS -fdefault-real-8 -O3 -funroll-all-loops -fcray-pointer -ffree-line-length-none -fallow-argument-mismatch
%DEBUG_FCFLAGS -fdefault-real-8 -O0 -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan
%FFLAGS %FCFLAGS
%LD %FC
%LDFLAGS
......
arch/arch-osx_gfortran_debug.fcm deleted 100644 → 0
View file @ dcfb5495
# generic gfortran compiler options for OSX installed with macport, http://www.macports.org/
#
# Prerequisite softwares installed with MacPorts :
# Prerequisite softwares installed with MacPorts :
# sudo port install gcc9
# sudo port install gcc_select
# sudo port select --set gcc mp-gcc9
# sudo port install mpich-gcc9
# sudo port install mpi_select
# sudo port select --set mpi mpich-gcc9-fortran
# sudo port install hdf5 +gcc9 +mpich +szip
# sudo port install netcdf +gcc9 +mpich
# sudo port install netcdf-fortran +gcc9 +mpich
# sudo port install p5.30-uri
#
# $ port select --show mpi
# The currently selected version for 'mpi' is 'mpich-gcc9-fortran'.
# $ port select --show gcc
# The currently selected version for 'gcc' is 'mp-gcc9'.
#
# Note that:
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
# - fcm variables are starting with a % (and not a $)
#
%NCDF_HOME /opt/local
%HDF5_HOME /opt/local
%XIOS_HOME /Users/$( whoami )/xios-trunk
%OASIS_HOME /not/defined
%NCDF_INC -I%NCDF_HOME/include -I%HDF5_HOME/include
%NCDF_LIB -L%NCDF_HOME/lib -lnetcdff -lnetcdf
%XIOS_INC -I%XIOS_HOME/inc
%XIOS_LIB -L%XIOS_HOME/lib -lxios -lstdc++
%OASIS_INC -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
%OASIS_LIB -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
%CPP cpp -Dkey_nosignedzero
%FC mpif90
%FCFLAGS -fdefault-real-8 -O0 -g -fbacktrace -funroll-all-loops -fcray-pointer -ffree-line-length-none -fcheck=all -finit-real=nan
%FFLAGS %FCFLAGS
%LD %FC
%LDFLAGS
%FPPFLAGS -P -traditional
%AR ar
%ARFLAGS rs
%MK make
%USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
%CC cc
%CFLAGS -O0
arch/misc/arch-X64_BULL.fcm
View file @ f6cac17d
......@@ -20,7 +20,7 @@
%FFLAGS %FCFLAGS
%LD scorep-mpiifort
%LDFLAGS -lstdc++
%FPPFLAGS -P -C -traditional -std=c99
%FPPFLAGS -P -traditional -std=c99
%AR ar
%ARFLAGS rs
%MK gmake
......
cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_cfg
View file @ f6cac17d
......@@ -117,6 +117,7 @@
!-----------------------------------------------------------------------
&namsbc_abl ! Atmospheric Boundary Layer formulation (ln_abl = T)
!-----------------------------------------------------------------------
cn_dom = 'dom_cfg_abl_L25Z10'
/
!-----------------------------------------------------------------------
&namtra_qsr ! penetrative solar radiation (ln_traqsr =T)
......
cfgs/ORCA2_ICE_PISCES/EXPREF/namelist_top_cfg
View file @ f6cac17d
......@@ -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)
......
cfgs/ORCA2_OFF_PISCES/EXPREF/namelist_top_cfg
View file @ f6cac17d
......@@ -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)
......
cfgs/SHARED/field_def_nemo-pisces.xml
View file @ f6cac17d
......@@ -276,20 +276,31 @@
<!-- dbio_T on T grid : variables available with diaar5 -->
<field id="TPP" long_name="Total Primary production of phyto" unit="mol/m3/s" grid_ref="grid_T_3D" />
<field id="TPNEW" long_name="New Primary production of phyto" unit="mol/m3/s" grid_ref="grid_T_3D" />
<field id="TPBFE" long_name="Total biogenic iron production" unit="mol/m3/s" grid_ref="grid_T_3D" />
<field id="INTDIC" long_name="DIC content" unit="kg/m2" />
<field id="O2MIN" long_name="Oxygen minimum concentration" unit="mol/m3" />
<field id="ZO2MIN" long_name="Depth of oxygen minimum concentration" unit="m" />
<field id="INTNFIX" long_name="Nitrogen fixation rate : vert. integrated" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > Nfix * e3t </field >
<field id="INTPPPHYN" long_name="Vertically integrated primary production by nanophy" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > PPPHYN * e3t </field >
<field id="INTPPPHYD" long_name="Vertically integrated primary production by diatom" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > PPPHYD * e3t </field >
<field id="INTPPPHYP" long_name="Vertically integrated primary production by picophy" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > PPPHYP * e3t </field >
<field id="INTPP" long_name="Vertically integrated primary production by phyto" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > TPP * e3t </field >
<field id="INTPNEW" long_name="Vertically integrated new primary production" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > TPNEW * e3t </field >
<field id="INTPBFE" long_name="Vertically integrated of biogenic iron production" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > TPBFE * e3t </field >
<field id="INTPBSI" long_name="Vertically integrated of biogenic Si production" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" > PBSi * e3t </field >
<field id="TPP" long_name="Total Primary production of phyto" unit="mol/m3/s" grid_ref="grid_T_3D" />
<field id="TPNEW" long_name="New Primary production of phyto" unit="mol/m3/s" grid_ref="grid_T_3D" />
<field id="TPBFE" long_name="Total biogenic iron production" unit="mol/m3/s" grid_ref="grid_T_3D" />
<field id="INTDIC" long_name="DIC content" unit="kg/m2" />
<field id="O2MIN" long_name="Oxygen minimum concentration" unit="mol/m3" />
<field id="ZO2MIN" long_name="Depth of oxygen minimum concentration" unit="m" />
<field id="Nfix_e3t" long_name="Nfix * e3t" unit="molN/m2/s" grid_ref="grid_T_3D" > Nfix * e3t </field >
<field id="PPPHYN_e3t" long_name="PPPHYN * e3t" unit="mol/m2/s" grid_ref="grid_T_3D" > PPPHYN * e3t </field >
<field id="PPPHYD_e3t" long_name="PPPHYD * e3t" unit="mol/m2/s" grid_ref="grid_T_3D" > PPPHYD * e3t </field >
<field id="PPPHYP_e3t" long_name="PPPHYP * e3t" unit="mol/m2/s" grid_ref="grid_T_3D" > PPPHYP * e3t </field >
<field id="PBSi_e3t" long_name="PBSi * e3t" unit="mol/m2/s" grid_ref="grid_T_3D" > PBSi * e3t </field >
<field id="TPP_e3t" long_name="TPP * e3t" unit="mol/m2/s" grid_ref="grid_T_3D" > TPP * e3t </field >
<field id="TPNEW_e3t" long_name="TPNEW * e3t" unit="mol/m2/s" grid_ref="grid_T_3D" > TPNEW * e3t </field >
<field id="TPBFE_e3t" long_name="TPBFE * e3t" unit="mol/m2/s" grid_ref="grid_T_3D" > TPBFE * e3t </field >
<field id="INTNFIX" long_name="Nitrogen fixation rate : vert. integrated" field_ref="Nfix_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<field id="INTPPPHYN" long_name="Vertically integrated primary production by nanophy" field_ref="PPPHYN_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<field id="INTPPPHYD" long_name="Vertically integrated primary production by diatom" field_ref="PPPHYD_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<field id="INTPPPHYP" long_name="Vertically integrated primary production by picophy" field_ref="PPPHYP_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<field id="INTPP" long_name="Vertically integrated primary production by phyto" field_ref="TPP_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<field id="INTPNEW" long_name="Vertically integrated new primary production" field_ref="TPNEW_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<field id="INTPBFE" long_name="Vertically integrated of biogenic iron production" field_ref="TPBFE_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<field id="INTPBSI" long_name="Vertically integrated of biogenic Si production" field_ref="PBSi_e3t" unit="mol/m2/s" grid_ref="grid_T_vsum" detect_missing_value="true" />
<!-- PISCES light : variables available with key_pisces_reduced -->
<field id="FNO3PHY" long_name="FNO3PHY" unit="" grid_ref="grid_T_3D" />
......
cfgs/SHARED/grid_def_nemo.xml
View file @ f6cac17d
......@@ -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>
<!-- -->
......
cfgs/SHARED/namelist_ref
View file @ f6cac17d
......@@ -326,6 +326,7 @@
nn_dyn_restore = 0 ! restoring option for dynamical ABL variables: = 0 no restoring
! = 1 equatorial restoring
! = 2 global restoring
rn_vfac = 0.
rn_ldyn_min = 4.5 ! dynamics nudging magnitude inside the ABL [hour] (~3 rn_Dt)
rn_ldyn_max = 1.5 ! dynamics nudging magnitude above the ABL [hour] (~1 rn_Dt)
rn_ltra_min = 4.5 ! tracers nudging magnitude inside the ABL [hour] (~3 rn_Dt)
......
doc/NEMO_manual_state.txt deleted 100644 → 0
View file @ dcfb5495
¤ 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
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**************************
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::
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<g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,
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<text x="16" y="15" fill="#010101"
fill-opacity=".3">
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<g fill="#fff" text-anchor="middle" font-family="DejaVu Sans,
Verdana,Geneva,sans-serif" font-size="11">
<text x="16" y="15" fill="#010101"
fill-opacity=".3">
DOI
</text>
<text x="16" y="14">
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y="15" fill="#010101" fill-opacity=".3">
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#!/bin/sh
## Avoid the use of shell builtin echo (for -e option)
alias echo='/bin/echo -e'
## Check dependancies
##-------------------
## Sphinx, BibTeX extension and "Read The Docs" theme
if [ -n "$( ./tools/check_pkg.py sphinx sphinxcontrib.bibtex sphinx_rtd_theme )" ]; then
echo 'One of the Python dependencies is missing => QUIT'
exit 2
fi
cd rst
echo "\t¤ Clean previous build"
make clean
echo
echo "\t¤ Generation of the guide"
make html > /dev/null
echo
echo "\t¤ End of building run"
echo "Open ./rst/build/html/NEMO_guide.html"
cd - > /dev/null
exit 0
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*.aux
*.bbl
*.blg
*.fdb*
*.fls
*.idx
*.ilg
*.ind
*.lo*
*.out
*.pdf
*.pyg
*.tdo
*.toc
*.xdv
cache*