Fix cdfpsi bug

Macrolib/macro.ukmo_gfortran

@@ -0,0 +1,15 @@
+# module load netcdf-fortran/4.6.1-gcc-12.2.0-43finqs gcc/13.2.0-gcc-12.2.0-lx4jx7u
+
+NCDF = -I${NETCDFF_ROOT}/include -L${NETCDFF_ROOT}/lib -lnetcdff
+
+NC4 = -D key_netcdf4
+#CMIP6 = -D key_CMIP6
+CMIP6 =
+
+F90=gfortran
+#OMP=-fopenmp
+OMP=
+FFLAGS= -O $(NCDF) $(NC4) -Wl,-rpath=${NETCDFF_ROOT}/lib -fno-second-underscore -ffree-line-length-256 $(OMP)
+
+#INSTALL=$(HOME)/local/bin
+#INSTALL_MAN=$(HOME)/local/man

README.md

@@ -1,16 +1,12 @@
-# CDFTOOLS
-  CDFTOOLS is a diagnostic package written in fortran 90 for the analysis of NEMO model output, initialized in  the frame of the DRAKKAR project (<https://www.drakkar-ocean.eu/>). It is now available on GitHub under the CeCILL license (<http://www.cecill.info/licences/Licence_CeCILL_V2-en.html>).
-
-  CDFTOOLS is an open source package and contributions from other group are welcomed. The Git workflow policy is still to be defined.
-
-  Actual version of CDFTOOLS is known as version 4. (See changes in paragraph *New features in version 4*, below).
-
+# CDFTOOLS - JMMP development branch
+   This is the main development branch of the JMMP FORK of [CDFTOOLS](https://github.com/meom-group/CDFTOOLS), a diagnostic package written in fortran 90 for the analysis of NEMO model output, initialized in the frame of the DRAKKAR project (<https://www.drakkar-ocean.eu/>). The main repository of CDFTOOLS is available on GitHub (<https://github.com/meom-group/CDFTOOLS>) under the CeCILL license (<http://www.cecill.info/licences/Licence_CeCILL_V2-en.html>). The current supported version of CDFTOOLS is version 4.
+
 ## Using CDFTOOLS
 
-#### Cloning the git repository
-To retrieve a copy of the CDFTOOLS source code and create a working directory, run the following on the command line: 
+#### Cloning the git JMMP development branch
+To retrieve a local copy of the CDFTOOLS `dev_jmmp` development branch run the following on the command line: 
 
-```> git clone https://github.com/meom-group/CDFTOOLS ```
+```> git clone -b dev_jmmp --single-branch https://github.com/JMMP-Group/CDFTOOLS.git CDFTOOLS_jmmp```
 
 #### Compiling CDFTOOLS
 All the fortran source are in src/ subdirectory. In src/ there is a Makefile for compiling the sources. The compiler/machines related definitions are supposed to be collected in a `make.macro` file. Some examples of `make.macro` are given in the Macrolib directory and can be used as template for a new compiler or new machine. Then the good practice is to make a link 

nam_cdf_names

@@ -0,0 +1,104 @@
+! ================================
+! cdftools namelist
+! ================================
+
+!---------------------------------------
+&namdim             ! Dimension names
+!---------------------------------------
+    cn_x = 'x'                  !: longitude
+    cn_y = 'y'                  !: latitude
+    cn_z = 'depth'              !: depth
+    cn_t = 'time_counter'       !: time
+/
+
+!---------------------------------------
+&namdimvar          ! Dimension variable names      
+!---------------------------------------
+    cn_vlon2d  = 'nav_lon'          !: longitude
+    cn_vlat2d  = 'nav_lat'          !: latitude
+
+    cn_vdeptht = 'deptht'
+    cn_vdepthu = 'depthu'
+    cn_vdepthv = 'depthv'
+    cn_vdepthw = 'depthw'                  !: depth
+
+    cn_vtimec  = 'time_centered'           !: time
+/
+
+!---------------------------------------
+&nammetrics         ! Mesh mask variable names
+!---------------------------------------
+    cn_ve1t = 'e1t'
+    cn_ve1u = 'e1u'
+    cn_ve1v = 'e1v'
+    cn_ve1f = 'e1f'      !: e1
+
+    cn_ve2t = 'e2t'
+    cn_ve2u = 'e2u'
+    cn_ve2v = 'e2v'
+    cn_ve2f = 'e2f'      !: e2
+
+    cn_ve3t1d = 'e3t'    !: e3 (1D)
+    cn_ve3w1d = 'e3w'    !: e3 (1D)
+    cn_ve3t = 'e3t_0'    !: e3 (3D)
+    cn_ve3u = 'e3u_0'    !: e3 (3D)
+    cn_ve3v = 'e3v_0'    !: e3 (3D)
+    cn_ve3w = 'e3w_0'    !: e3 (3D)
+
+    cn_vff  = 'ff_f'     !: f^2
+
+    cn_glamt = 'glamt'
+    cn_glamu = 'glamu'
+    cn_glamv = 'glamv'
+    cn_glamf = 'glamf'   !: longitude
+
+    cn_gphit = 'gphit'
+    cn_gphiu = 'gphiu'
+    cn_gphiv = 'gphiv'
+    cn_gphif = 'gphif'   !: latitude
+
+    cn_gdept = 'gdept'                              
+    cn_gdepw = 'gdepw'   !: 1d dep variable         
+
+    cn_hdept = 'hdept'
+    cn_hdepw = 'hdepw'   !: 2d dep variable
+/
+
+!---------------------------------------
+&namvars            ! Variable names                
+!---------------------------------------
+    cn_votemper  = 'thetao_con' !: conservative temperature
+    cn_vosaline  = 'so_abs'     !: absolute salinity
+    cn_vozocrtx  = 'uo'         !: zonal velocity
+    cn_vomecrty  = 'vo'         !: meridional velocity
+    cn_sozotaux  = 'tauuo'      !: zonal wind stress 
+/
+
+!---------------------------------------
+&nambathy           ! Bathymetry file and variable names
+!---------------------------------------
+   cn_bathymet  = 'bathy_metry'
+/
+
+!---------------------------------------
+&namsqdvar          ! Squared variable names
+!---------------------------------------
+/
+
+!---------------------------------------
+&namcubvar          ! Cubed variable names
+!---------------------------------------
+/
+
+!---------------------------------------
+&nammeshmask        ! Mesh mask file names          
+!---------------------------------------
+    cn_fzgr    = 'mesh_mask.nc'    !: vertical mesh file
+    cn_fhgr    = 'mesh_mask.nc'    !: horizontal mesh file
+    cn_fmsk    = 'mesh_mask.nc'    !: mesh mask file
+/
+
+!---------------------------------------
+&nammeshmask_var    ! Basin mask names
+!---------------------------------------
+/

src/Makefile

@@ -287,8 +287,8 @@ cdfvtrp: cdfio.o  cdfvtrp.f90
 cdfpsi: cdfio.o  modutils.o cdfpsi.f90
 	$(F90) cdfpsi.f90  -o $(BINDIR)/cdfpsi cdfio.o modcdfnames.o modutils.o $(FFLAGS)
 
-cdftransport: cdfio.o  modutils.o cdftransport.f90
-	$(F90) cdftransport.f90 -o $(BINDIR)/cdftransport cdfio.o modcdfnames.o modutils.o $(FFLAGS)
+cdftransport: cdfio.o  modutils.o cdftools.o cdftransport.f90
+	$(F90) cdftransport.f90 -o $(BINDIR)/cdftransport cdfio.o modcdfnames.o modutils.o cdftools.o $(FFLAGS)
 
 cdfvFWov: cdfio.o  modutils.o cdfvFWov.f90
 	$(F90) cdfvFWov.f90 -o $(BINDIR)/cdfvFWov cdfio.o modcdfnames.o modutils.o $(FFLAGS)

src/cdfio.F90

@@ -1422,7 +1422,7 @@ FUNCTION FindVarName(cdfile,cdvar,ld_verbose)
 
   END FUNCTION FindVarName
 
-  FUNCTION  getvar (cdfile,cdvar,klev,kpi,kpj,kimin,kjmin, ktime, ldiom)
+  FUNCTION  getvar (cdfile,cdvar,klev,kpi,kpj,kimin,kjmin, ktime, ldiom, ld_zeromask)
     !!---------------------------------------------------------------------
     !!                  ***  FUNCTION  getvar  ***
     !!
@@ -1443,6 +1443,7 @@ FUNCTION  getvar (cdfile,cdvar,klev,kpi,kpj,kimin,kjmin, ktime, ldiom)
     INTEGER(KIND=4), OPTIONAL, INTENT(in) :: kimin, kjmin ! Optional variable. If missing 1 is assumed
     INTEGER(KIND=4), OPTIONAL, INTENT(in) :: ktime        ! Optional variable. If missing 1 is assumed
     LOGICAL,         OPTIONAL, INTENT(in) :: ldiom        ! Optional variable. If missing false is assumed
+    LOGICAL,         OPTIONAL, INTENT(in) :: ld_zeromask   ! Optional variable. Reset field to zero at missing value points. If missing false is assumed
     REAL(KIND=4), DIMENSION(kpi,kpj) :: getvar            ! 2D REAL 4 holding variable field at klev
 
     INTEGER(KIND=4), DIMENSION(4)               :: istart, icount, inldim
@@ -1454,7 +1455,7 @@ FUNCTION  getvar (cdfile,cdvar,klev,kpi,kpj,kimin,kjmin, ktime, ldiom)
     REAL(KIND=4)                                :: spval  !: missing value
     REAL(KIND=4) , DIMENSION (:,:), ALLOCATABLE :: zend, zstart
     CHARACTER(LEN=256)                          :: clvar
-    LOGICAL                                     :: lliom=.false., llperio=.false.
+    LOGICAL                                     :: lliom=.false., llperio=.false., ll_zeromask=.false.
     LOGICAL                                     :: llog=.FALSE. , lsf=.FALSE. , lao=.FALSE.
     !!
     INTEGER(KIND=4)                :: ityp
@@ -1499,6 +1500,12 @@ FUNCTION  getvar (cdfile,cdvar,klev,kpi,kpj,kimin,kjmin, ktime, ldiom)
        lliom=.false.
     ENDIF
 
+    IF (PRESENT(ld_zeromask) ) THEN
+       ll_zeromask=ld_zeromask
+    ELSE
+       ll_zeromask=.false.
+    ENDIF
+
     ! Must reset the flags to false for every call to getvar
     clvar=cdvar
     llog = .FALSE.
@@ -1603,7 +1610,8 @@ FUNCTION  getvar (cdfile,cdvar,klev,kpi,kpj,kimin,kjmin, ktime, ldiom)
     IF (lsf )  WHERE (getvar /= spval )  getvar=getvar*sf
     IF (lao )  WHERE (getvar /= spval )  getvar=getvar + ao
     IF (llog)  WHERE (getvar /= spval )  getvar=10**getvar
-
+    IF (ll_zeromask) WHERE (getvar == spval ) getvar=0.0
+
     istatus=NF90_CLOSE(incid)
 
   END FUNCTION getvar
@@ -1981,13 +1989,13 @@ FUNCTION  getvarxz (cdfile, cdvar, kj, kpi, kpz, kimin, kkmin, ktime)
     lao=.FALSE.
 
     clvar=cdvar
-    IF ( clvar == cn_ve3v) THEN
-    SELECT CASE ( cg_zgr_ver )
-    CASE ( 'v2.0' ) ; clvar = 'e3v_ps'
-    CASE ( 'v3.0' ) ; clvar = 'e3v'
-    CASE ( 'v3.6' ) ; clvar = 'e3v_0'
-    END SELECT
-    ENDIF
+    !IF ( clvar == cn_ve3v) THEN
+    !SELECT CASE ( cg_zgr_ver )
+    !CASE ( 'v2.0' ) ; clvar = 'e3v_ps'
+    !CASE ( 'v3.0' ) ; clvar = 'e3v'
+    !CASE ( 'v3.6' ) ; clvar = 'e3v_0'
+    !END SELECT
+    !ENDIF
 
     CALL ERR_HDL(NF90_OPEN(cdfile,NF90_NOWRITE,incid) )
     CALL ERR_HDL(NF90_INQ_VARID ( incid,clvar,id_var))

src/cdfpsi.f90

@@ -243,6 +243,7 @@ PROGRAM cdfpsi
 
   CALL CreateOutput
 
+  PRINT *, 'Getting ',TRIM(cn_ve1v), TRIM(cn_ve2u)
   e1v(:,:)   = getvar(cn_fhgr, cn_ve1v, 1, npiglo, npjglo)
   e2u(:,:)   = getvar(cn_fhgr, cn_ve2u, 1, npiglo, npjglo)
   IF ( lmask) THEN
@@ -270,7 +271,7 @@ PROGRAM cdfpsi
 
      DO jk = 1,npk
         IF ( ll_v ) THEN
-           zv(:,:) = getvar(cf_vfil, cn_vomecrty, jk, npiglo, npjglo, ktime=jt )
+           zv(:,:) = getvar(cf_vfil, cn_vomecrty, jk, npiglo, npjglo, ktime=jt, ld_zeromask=.true. )
            IF ( lfull ) THEN ; e3v(:,:) = e31d(jk)
            ELSE              ; e3v(:,:) = getvar(cn_fe3v, cn_ve3v, jk, npiglo, npjglo, ktime=it, ldiom=.NOT.lg_vvl)
            ENDIF
@@ -289,7 +290,8 @@ PROGRAM cdfpsi
         ENDIF
 
         IF ( ll_u) THEN
-           zu(:,:) = getvar(cf_ufil, cn_vozocrtx, jk, npiglo, npjglo, ktime=jt )
+           zu(:,:) = getvar(cf_ufil, cn_vozocrtx, jk, npiglo, npjglo, ktime=jt, ld_zeromask=.true. )
+           PRINT *, 'Getting ',TRIM(cn_ve3u)
            IF ( lfull ) THEN ; e3u(:,:) = e31d(jk)
            ELSE              ; e3u(:,:) = getvar(cn_fe3u, cn_ve3u, jk, npiglo, npjglo, ktime=it, ldiom=.NOT.lg_vvl)
            ENDIF

src/cdfsigtrp.f90

@@ -285,11 +285,10 @@ PROGRAM cdfsigtrp
   lchk = lchk .OR. chkfile( cf_vfil    )
   IF ( lchk ) STOP 99 ! missing file
 
-   ! Look for missing value for salinity, U and V
-   zsps = getspval(cf_sfil, cn_vosaline )
-   zspu = getspval(cf_ufil, cn_vozocrtx )
-   zspv = getspval(cf_vfil, cn_vomecrty )
-
+  ! Look for missing value for salinity, U and V
+  zsps = getspval(cf_sfil, cn_vosaline )
+  zspu = getspval(cf_ufil, cn_vozocrtx )
+  zspv = getspval(cf_vfil, cn_vomecrty )
 
   IF ( lg_vvl )  THEN
      cn_fe3u = cf_ufil
@@ -327,8 +326,9 @@ PROGRAM cdfsigtrp
   ! Initialise sections from file 
   ! first call to get nsection and allocate arrays 
   IF ( lbrk ) THEN 
-     npiglo = getdim (cf_brk, cn_x)
-     nsection = 1 ; iimina=1 ; iimaxa=npiglo ; ijmina=1 ; ijmaxa=1
+     !npiglo = getdim (cf_brk, cn_x)
+     !nsection = 1 ; iimina=1 ; iimaxa=npiglo ; ijmina=1 ; ijmaxa=1
+     nsection = 1
   ELSE             
      nsection = 0 
      CALL section_init(cf_section, csection,cvarname,clongname,iimina, iimaxa, ijmina, ijmaxa, nsection)