First commit. Add build + essential getting started config files

MY_SRC/tideini.F90

+MODULE tideini
+   !!======================================================================
+   !!                       ***  MODULE  tideini  ***
+   !! Initialization of tidal forcing
+   !!======================================================================
+   !! History :  1.0  !  2007  (O. Le Galloudec)  Original code
+   !!----------------------------------------------------------------------
+   USE oce            ! ocean dynamics and tracers variables
+   USE dom_oce        ! ocean space and time domain
+   USE phycst         ! physical constant
+   USE daymod         ! calandar
+   USE tide_mod       ! 
+   !
+   USE in_out_manager ! I/O units
+   USE iom            ! xIOs server
+   USE ioipsl         ! NetCDF IPSL library
+   USE lbclnk         ! ocean lateral boundary conditions (or mpp link)
+
+   IMPLICIT NONE
+   PUBLIC
+
+   REAL(wp), PUBLIC, ALLOCATABLE, DIMENSION(:) ::   omega_tide   !:
+   REAL(wp), PUBLIC, ALLOCATABLE, DIMENSION(:) ::   v0tide       !:
+   REAL(wp), PUBLIC, ALLOCATABLE, DIMENSION(:) ::   utide        !:
+   REAL(wp), PUBLIC, ALLOCATABLE, DIMENSION(:) ::   ftide        !:
+
+   LOGICAL , PUBLIC ::   ln_tide         !:
+   LOGICAL , PUBLIC ::   ln_tide_pot     !:
+   LOGICAL , PUBLIC ::   ln_tide_ramp    !:
+   INTEGER , PUBLIC ::   nb_harmo        !:
+   INTEGER , PUBLIC ::   kt_tide         !:
+   REAL(wp), PUBLIC ::   rdttideramp     !:
+   ! NB - read love number from namelist
+   REAL(wp), PUBLIC ::   dn_love_number  !:
+   ! END NB
+   INTEGER , PUBLIC, ALLOCATABLE, DIMENSION(:) ::   ntide   !:
+
+   !!----------------------------------------------------------------------
+   !! NEMO/OPA 3.5 , NEMO Consortium (2013)
+   !! $Id: tideini.F90 7646 2017-02-06 09:25:03Z timgraham $
+   !! Software governed by the CeCILL licence     (NEMOGCM/NEMO_CeCILL.txt)
+   !!----------------------------------------------------------------------
+CONTAINS
+   
+   SUBROUTINE tide_init
+      !!----------------------------------------------------------------------
+      !!                 ***  ROUTINE tide_init  ***
+      !!----------------------------------------------------------------------      
+      INTEGER  :: ji, jk
+      CHARACTER(LEN=4), DIMENSION(jpmax_harmo) :: clname
+      INTEGER  ::   ios                 ! Local integer output status for namelist read
+      !
+      ! NB - read love number from namelist
+      !NAMELIST/nam_tide/ln_tide, ln_tide_pot, ln_tide_ramp, rdttideramp, clname
+      NAMELIST/nam_tide/ln_tide, ln_tide_pot, ln_tide_ramp, rdttideramp, dn_love_number, clname
+      ! END NB
+      !!----------------------------------------------------------------------
+      !
+      ! Read Namelist nam_tide
+      REWIND( numnam_ref )              ! Namelist nam_tide in reference namelist : Tides
+      READ  ( numnam_ref, nam_tide, IOSTAT = ios, ERR = 901)
+901   IF( ios /= 0 )   CALL ctl_nam ( ios , 'nam_tide in reference namelist', lwp )
+      !
+      REWIND( numnam_cfg )              ! Namelist nam_tide in configuration namelist : Tides
+      READ  ( numnam_cfg, nam_tide, IOSTAT = ios, ERR = 902 )
+902   IF( ios /= 0 )   CALL ctl_nam ( ios , 'nam_tide in configuration namelist', lwp )
+      IF(lwm) WRITE ( numond, nam_tide )
+      !
+      IF (ln_tide) THEN
+         IF (lwp) THEN
+            WRITE(numout,*)
+            WRITE(numout,*) 'tide_init : Initialization of the tidal components'
+            WRITE(numout,*) '~~~~~~~~~ '
+            WRITE(numout,*) '   Namelist nam_tide'
+            WRITE(numout,*) '              Use tidal components : ln_tide      = ', ln_tide
+            WRITE(numout,*) '      Apply astronomical potential : ln_tide_pot  = ', ln_tide_pot
+!            WRITE(numout,*) '                                     nb_harmo     = ', nb_harmo
+            WRITE(numout,*) '                                     ln_tide_ramp = ', ln_tide_ramp
+! NB - Love number
+            WRITE(numout,*) '                                     dn_love_number = ', dn_love_number
+! End NB
+         ENDIF
+      ELSE
+         IF(lwp) WRITE(numout,*)
+         IF(lwp) WRITE(numout,*) 'tide_init : tidal components not used (ln_tide = F)'
+         IF(lwp) WRITE(numout,*) '~~~~~~~~~ '
+         RETURN
+      ENDIF
+      !
+      CALL tide_init_Wave
+      !
+      nb_harmo=0
+      DO jk = 1, jpmax_harmo
+         DO ji = 1,jpmax_harmo
+            IF( TRIM(clname(jk)) == Wave(ji)%cname_tide )   nb_harmo = nb_harmo + 1
+         END DO
+      END DO
+      IF (ln_tide .and.lwp) WRITE(numout,*) '                                     nb_harmo     = ', nb_harmo
+
+      ! Ensure that tidal components have been set in namelist_cfg
+      IF( nb_harmo == 0 )   CALL ctl_stop( 'tide_init : No tidal components set in nam_tide' )
+      !
+      IF( ln_tide_ramp.AND.((nitend-nit000+1)*rdt/rday < rdttideramp) )   &
+         &   CALL ctl_stop('rdttideramp must be lower than run duration')
+      IF( ln_tide_ramp.AND.(rdttideramp<0.) ) &
+         &   CALL ctl_stop('rdttideramp must be positive')
+      !
+      ALLOCATE( ntide(nb_harmo) )
+      DO jk = 1, nb_harmo
+         DO ji = 1, jpmax_harmo
+            IF( TRIM(clname(jk)) == Wave(ji)%cname_tide ) THEN
+               ntide(jk) = ji
+               EXIT
+            ENDIF
+         END DO
+      END DO
+      !
+      ALLOCATE( omega_tide(nb_harmo), v0tide    (nb_harmo),   &
+         &      utide     (nb_harmo), ftide     (nb_harmo)  )
+      kt_tide = nit000
+      !
+   END SUBROUTINE tide_init
+     
+   !!======================================================================
+END MODULE tideini

MY_SRC/usrdef_istate.F90

+MODULE usrdef_istate
+   !!======================================================================
+   !!                   ***  MODULE  usrdef_istate   ***
+   !!
+   !!                     ===  GYRE configuration  ===
+   !!
+   !! User defined : set the initial state of a user configuration
+   !!======================================================================
+   !! History :  NEMO ! 2016-03  (S. Flavoni) Original code
+   !!----------------------------------------------------------------------
+
+   !!----------------------------------------------------------------------
+   !!  usr_def_istate : initial state in Temperature and salinity
+   !!----------------------------------------------------------------------
+   USE par_oce        ! ocean space and time domain
+   USE phycst         ! physical constants
+   !
+   USE in_out_manager ! I/O manager
+   USE lib_mpp        ! MPP library
+   
+   IMPLICIT NONE
+   PRIVATE
+
+   PUBLIC   usr_def_istate   ! called in istate.F90
+
+   !!----------------------------------------------------------------------
+   !! NEMO/OPA 4.0 , NEMO Consortium (2016)
+   !! $Id$ 
+   !! Software governed by the CeCILL licence     (NEMOGCM/NEMO_CeCILL.txt)
+   !!----------------------------------------------------------------------
+CONTAINS
+  
+   SUBROUTINE usr_def_istate( pdept, ptmask, pts, pu, pv, pssh )
+      !!----------------------------------------------------------------------
+      !!                   ***  ROUTINE usr_def_istate  ***
+      !! 
+      !! ** Purpose :   Initialization of the dynamics and tracers
+      !!                Here GYRE configuration example : (double gyre with rotated domain)
+      !!
+      !! ** Method  : - set temprature field
+      !!              - set salinity   field
+      !!----------------------------------------------------------------------
+      REAL(wp), DIMENSION(jpi,jpj,jpk)     , INTENT(in   ) ::   pdept   ! depth of t-point               [m]
+      REAL(wp), DIMENSION(jpi,jpj,jpk)     , INTENT(in   ) ::   ptmask  ! t-point ocean mask             [m]
+      REAL(wp), DIMENSION(jpi,jpj,jpk,jpts), INTENT(  out) ::   pts     ! T & S fields      [Celsius ; g/kg]
+      REAL(wp), DIMENSION(jpi,jpj,jpk)     , INTENT(  out) ::   pu      ! i-component of the velocity  [m/s] 
+      REAL(wp), DIMENSION(jpi,jpj,jpk)     , INTENT(  out) ::   pv      ! j-component of the velocity  [m/s] 
+      REAL(wp), DIMENSION(jpi,jpj)         , INTENT(  out) ::   pssh    ! sea-surface height
+      !
+      INTEGER :: ji, jj, jk  ! dummy loop indices
+      !!----------------------------------------------------------------------
+      !
+      IF(lwp) WRITE(numout,*)
+      IF(lwp) WRITE(numout,*) 'usr_def_istate : analytical definition of initial state '
+      IF(lwp) WRITE(numout,*) '~~~~~~~~~~~~~~   Ocean at rest, with an horizontally uniform T and S profiles'
+      !
+      pu  (:,:,:) = 0._wp        ! ocean at rest
+      pv  (:,:,:) = 0._wp
+      pssh(:,:)   = 0._wp
+      !
+      DO jk = 1, jpk             ! horizontally uniform T & S profiles
+         DO jj = 1, jpj
+            DO ji = 1, jpi
+               pts(ji,jj,jk,jp_tem) = 20._wp * ptmask(ji,jj,jk)
+               pts(ji,jj,jk,jp_sal) = 36.25_wp * ptmask(ji,jj,jk)
+            END DO
+         END DO
+      END DO
+      !   
+   END SUBROUTINE usr_def_istate
+
+   !!======================================================================
+END MODULE usrdef_istate

MY_SRC/usrdef_sbc.F90

+MODULE usrdef_sbc
+   !!======================================================================
+   !!                       ***  MODULE usrdef_sbc  ***
+   !! 
+   !!                  ===  WAD_TEST_CASES configuration  ===
+   !!
+   !! User defined :   surface forcing of a user configuration
+   !!======================================================================
+   !! History :  4.0   ! 2016-03  (S. Flavoni, G. Madec)  user defined interface
+   !!----------------------------------------------------------------------
+
+   !!----------------------------------------------------------------------
+   !!   usrdef_sbc     : user defined surface bounday conditions in WAD_TEST_CASES case
+   !!----------------------------------------------------------------------
+   USE oce             ! ocean dynamics and tracers
+   USE dom_oce         ! ocean space and time domain
+   USE sbc_oce         ! Surface boundary condition: ocean fields
+   USE phycst          ! physical constants
+   !
+   USE in_out_manager  ! I/O manager
+   USE lib_mpp         ! distribued memory computing library
+   USE lbclnk          ! ocean lateral boundary conditions (or mpp link)
+   USE lib_fortran     ! Fortran utilities (allows no signed zero when 'key_nosignedzero' defined) 
+
+   IMPLICIT NONE
+   PRIVATE
+
+   PUBLIC   usrdef_sbc_oce    ! routine called in sbcmod module
+   PUBLIC   usrdef_sbc_ice_tau  ! routine called by sbcice_lim.F90 for ice dynamics
+   PUBLIC   usrdef_sbc_ice_flx  ! routine called by sbcice_lim.F90 for ice thermo
+
+   !! * Substitutions
+#  include "vectopt_loop_substitute.h90"
+   !!----------------------------------------------------------------------
+   !! NEMO/OPA 4.0 , NEMO Consortium (2016)
+   !! $Id$
+   !! Software governed by the CeCILL licence     (NEMOGCM/NEMO_CeCILL.txt)
+   !!----------------------------------------------------------------------
+CONTAINS
+
+   SUBROUTINE usrdef_sbc_oce( kt )
+      !!---------------------------------------------------------------------
+      !!                    ***  ROUTINE usr_def_sbc  ***
+      !!              
+      !! ** Purpose :   provide at each time-step the surface boundary
+      !!              condition, i.e. the momentum, heat and freshwater fluxes.
+      !!
+      !! ** Method  :   all 0 fields, for WAD_TEST_CASES case
+      !!                CAUTION : never mask the surface stress field !
+      !!
+      !! ** Action  : - set to ZERO all the ocean surface boundary condition, i.e.   
+      !!                   utau, vtau, taum, wndm, qns, qsr, emp, sfx
+      !!
+      !!----------------------------------------------------------------------
+      INTEGER, INTENT(in) ::   kt   ! ocean time step
+      !!---------------------------------------------------------------------
+      !
+      IF( kt == nit000 ) THEN
+         !
+         IF(lwp) WRITE(numout,*)' usr_sbc : WAD_TEST_CASES case: NO surface forcing'
+         IF(lwp) WRITE(numout,*)' ~~~~~~~~~~~   utau = vtau = taum = wndm = qns = qsr = emp = sfx = 0'
+         !
+         utau(:,:) = 0._wp
+         vtau(:,:) = 0._wp
+         taum(:,:) = 0._wp
+         wndm(:,:) = 0._wp
+         !
+         emp (:,:) = 0._wp
+         sfx (:,:) = 0._wp
+         qns (:,:) = 0._wp
+         qsr (:,:) = 0._wp
+         !         
+      ENDIF
+      !
+   END SUBROUTINE usrdef_sbc_oce
+
+   SUBROUTINE usrdef_sbc_ice_tau( kt )
+      INTEGER, INTENT(in) ::   kt   ! ocean time step
+   END SUBROUTINE usrdef_sbc_ice_tau
+
+   SUBROUTINE usrdef_sbc_ice_flx( kt )
+      INTEGER, INTENT(in) ::   kt   ! ocean time step
+   END SUBROUTINE usrdef_sbc_ice_flx
+
+   !!======================================================================
+END MODULE usrdef_sbc

README

+THIS IS WORK IN PROGRESS. I.e. IT SEEMS LIKE A GOOD IDEA BUT IS NOT COMPLETE OR IN A SETTLED FORMAT
+
+
+EXP00
+=====
+
+Main dev directory
+
+
+EXP01
+=====
+25 Jan 18
+Experiments to test rn_rdt limits.
+Also turing on lateral diffusion of momentum.
+
+
+
+
+!-----------------------------------------------------------------------
+&namtra_ldf    !   lateral diffusion scheme for tracers                 (default: NO diffusion)
+!-----------------------------------------------------------------------
+   !                       !  Operator type:
+   !                           !  no diffusion: set ln_traldf_lap=..._blp=F
+   ln_traldf_lap   =  .true.  !    laplacian operator
+   ln_traldf_blp   =  .false.  !  bilaplacian operator
+   !
+   !                       !  Direction of action:
+   ln_traldf_lev   =  .false.  !  iso-level
+   ln_traldf_hor   =  .false.  !  horizontal (geopotential)
+   ln_traldf_iso   =  .true.  !  iso-neutral (standard operator)
+   ln_traldf_triad =  .false.  !  iso-neutral (triad    operator)
+
+
+
+   rn_rdt      =  360.     !  time step for the dynamics (and tracer if nn_acc=0)
+dt=360 blew up.
+Trying 300s. bloew up
+Trying 200s. Blews up at kt=26
+
+
+EXP_hpg_err
+==========
+No forcing. T(z),S(z) profiles. Clamped T(z),S(z) boundaries. Start from rest.
+Compiled without tidal analysis: I.e. NO key_harm_ana
+EXEC: nemo_notide_TSprofile.exe
+
+nt = 1200, dt=6mins. 5 days in 20 mins
+--> 2*30 days in 2*2 hours. nt = 2*7200
+
+Plan: grep Umax from solver.stat  Check for stability.
+
+EXP_tideonly
+============
+
+Only tidal forcing. constant T and S
+Include: key_harm_ana
+EXEC: nemo_tideonyl_TSconst.exe
+
+

README.md

+# NEMO_cfgs
+NEMO BoBEAS configuration
+
+Each configuration directory should be laid out in the following manner, to
+facilitate configuration archival and sharing:
+
+<pre>
+BoBEAS
+|____ARCH
+| |____arch-XC_ARCHER.fcm
+|____arch_xios
+| |____arch-XC_ARCHER.env
+| |____arch-XC_ARCHER.fcm
+| |____arch-XC_ARCHER.path
+|____cpp_MYCONFIG.fcm
+!____EXP_README.txt
+|____EXP00
+| |____1_namelist_cfg
+| |____1_namelist_ice_cfg
+| |____1_namelist_ice_ref
+| |____1_namelist_ref
+| |____context_nemo.xml
+| |____domain_def_nemo.xml
+| |____field_def_nemo-lim.xml
+| |____field_def_nemo-opa.xml
+| |____field_def_nemo-pisces.xml
+| |____file_def_nemo.xml
+| |____iodef.xml
+| |____namelist_cfg
+| |____namelist_ice_cfg
+| |____namelist_ice_ref
+| |____namelist_pisces_cfg
+| |____namelist_pisces_ref
+| |____namelist_ref
+| |____namelist_top_cfg
+| |____namelist_top_ref
+| |____runscript
+|____MY_SRC
+| |____*.F90
+|____INPUTS
+| |____namelist.bdy
+|____README.md
+</pre>

arch_xios/arch-XC30_ARCHER.env

+export HDF5_INC_DIR=${HDF5_DIR}/include
+export HDF5_LIB_DIR=${HDF5_DIR}/lib
+export NETCDF_INC_DIR=${NETCDF_DIR}/include
+export NETCDF_LIB_DIR=${NETCDF_DIR}/lib

arch_xios/arch-XC30_ARCHER.fcm

+%CCOMPILER           CC
+%FCOMPILER           ftn
+%LINKER              ftn -nofor-main -v
+
+%BASE_CFLAGS
+%PROD_CFLAGS    -O3 -D BOOST_DISABLE_ASSERTS
+%DEV_CFLAGS     -g -traceback
+%DEBUG_CFLAGS   -DBZ_DEBUG -g -traceback -fno-inline
+
+%BASE_FFLAGS    -D__NONE__
+%PROD_FFLAGS    -O2
+%DEV_FFLAGS     -g -O2 -traceback
+%DEBUG_FFLAGS   -g -traceback
+
+%BASE_INC       -D__NONE__
+%BASE_LD        -lstdc++
+
+%CPP            CC -EP
+%FPP            cpp -P
+%MAKE           gmake

arch_xios/arch-XC30_ARCHER.path

+NETCDF_INCDIR="-I $NETCDF_INC_DIR"
+NETCDF_LIBDIR='-Wl,"--allow-multiple-definition" -Wl,"-Bstatic" -L $NETCDF_LIB_DIR'
+NETCDF_LIB="-lnetcdf -lnetcdff"
+
+MPI_INCDIR=""
+MPI_LIBDIR=""
+MPI_LIB=""
+
+#HDF5_INCDIR="-I $HDF5_INC_DIR"
+HDF5_LIBDIR="-L $HDF5_LIB_DIR"
+HDF5_LIB="-lhdf5_hl -lhdf5 -lz"
+
+OASIS_INCDIR=""
+OASIS_LIBDIR=""
+OASIS_LIB=""
+#OASIS_INCDIR="-I$PWD/../../prism/X64/build/lib/psmile.MPI1"
+#OASIS_LIBDIR="-L$PWD/../../prism/X64/lib"
+#OASIS_LIB="-lpsmile.MPI1 -lmpp_io"

cpp_INDIAN_OCEAN.fcm

+bld::tool::fppkeys key_zdfgls \
+key_FES14_tides \
+key_diaharm_fast \
+key_mpp_mpi \
+key_iomput \
+key_nosignedzero