Merge remote-tracking branch 'origin/develop' into syncdev2ufs_2023jun27

* origin/develop:
  handle NaN air-sea temperatures from nearest land points (NOAA-EMC#869)
  Increase valid_max for f in ounp (NOAA-EMC#1014)
  Bugfix deallocation of invalid memory in ww3_prnc (NOAA-EMC#1016)
  Update to orion intel module path and two typo corrections. (NOAA-EMC#1011)
  Bugfix to out of bounds array write in w3profsmd_pdlib.f90 (NOAA-EMC#1013)
  Simple logic fix for time interpolation of boundary nodes at the end of W3XYPFSNIMP. (NOAA-EMC#1005)
  in w3iors use NSEA instead of NSEAL in serial write/read of VA (NOAA-EMC#954)
  Update documentation for UNST namelist (NOAA-EMC#986)
  In certain coupled configurations, the piece of code testing the coupling frequency to check if 'receive' coupling exchanges need to take place fail, resulting in an infinite loop causing the integration between time zero and the first time step to repeat indefinitely. This check needs to be rewritten, which fixes also issue NOAA-EMC#816 in a simpler way.  (NOAA-EMC#999)

model/inp/ww3_grid.inp

@@ -305,33 +305,44 @@ $   limitation and the GSE alleviation.
 $
 $ Unstructured grids ------------------------------------------------ $
 $   UNST parameters       : Namelist UNST
-$                           UGOBCAUTO  : TRUE: OBC points are taken from  type 15 elements
-$                                       FALSE: OBC points must be listed in ww3_grid.inp
-$                           UGOBCDEPTH : Threshold ( < 0) depth for OBC points if UGOBCAUTO is TRUE
-$                           UGOBCFILE : Reading boundary files from a file
-$                           EXPFSN  : Activation of N scheme (only one of the below 4, True - Active, False - not active)
+$                           UGBCCFL    : Turns on/off (TRUE/FALSE) the computation of the CFL number on the physical domain boundary. 
+$                                        If FALSE the explicit scheme can be much faster though stability is not guaranteed
+$                                        (default TRUE)
+$                           UGOBCAUTO  : TRUE: OBC points are taken from  type 15 elements (default)
+$                                        FALSE: OBC points must be listed in ww3_grid.inp
+$                           UGOBCDEPTH : Threshold ( < 0) depth (default -10) for OBC points if UGOBCAUTO is TRUE
+$                           UGOBCFILE  : File name of file for reading boudary (default 'unset') 
+$
+$                           The following are TRUE/FALSE variables and only one can be TRUE. 
+$                           By default, EXPFSN is TRUE and must be set to false to activate another option  
+$                           EXPFSN    : Activation of N scheme (default option)
 $                           EXPFSPSI  : Activation of PSI scheme
 $                           EXPFSFCT  : Activation of FCT scheme
-$                           IMPFSN  : Activation of N implicit scheme
-$                           EXPTOTAL  : Activation of the Block explicit N scheme solver
-$                           IMPTOTAL  : Activation of fully implicit scheme | Non splitting
-$                           IMPREFRACTION : Turn on implicit freq. shift (only with imptotal)
-$                           IMPFREQSHIFT  : Turn on implicit freq. shift terms (only with imptotal)
-$                           IMPSOURCE     : Turn on implicit source terms (only with imptotal)
-$                           JGS_TERMINATE_MAXITER  : max. Number of iterations
-$                           JGS_TERMINATE_DIFFERENCE  : Terminate based on the total change of the unweightet sum of wave action
-$                           JGS_TERMINATE_NORM  : Terminate based on the norm of the solution
-$                           JGS_USE_JACOBI  : Use Jacobi solver family
-$                           JGS_BLOCK_GAUSS_SEIDEL  : Use Block Gauss Seidel method for imptotal instead of the conservative jacobi iterator.
-$                           JGS_MAXITER  : max. Number of solver iterations
-$                           JGS_PMIN  : % of grid points that do not need to converge during solver iteration.
-$                           JGS_DIFF_THR  : implicit solver threshold for JGS_TERMINATE_DIFFERENCE
-$                           JGS_NORM_THR  : terminate based on the norm of the solution
-$                           JGS_LIMITER  : use total (quasi-steady: limits whole equation) instead of local limiter (un-steady: limits only source terms)
-$                           JGS_LIMITER_FUNC  : 1 - old limiter; 2 - alternatnive limiter
-$                           SETUP_APPLY_WLV  : Compute wave setup (experimental)
-$                           SOLVERTHR_SETUP  : Solver threshold for setup computations
-$                           CRIT_DEP_SETUP  : Critical depths for setup computations
+$                           IMPFSN    : Activation of N implicit scheme
+$                           EXPTOTAL  : Activation of Block explicit N scheme solver
+$                           IMPTOTAL  : Activation of fully implicit scheme, non splitting
+$                             
+$                           The following TRUE/FALSE variables are only for IMPTOTAL=TRUE
+$                           IMPREFRACTION : Turn on implicit freq. shift (default FALSE) 
+$                           IMPFREQSHIFT  : Turn on implicit freq. shift terms (default FALSE)
+$                           IMPSOURCE     : Turn on implicit source terms (default FALSE)
+$
+$                           JGS_TERMINATE_MAXITER  : Terminate based on max number of iterations (TRUE/FALSE, default TRUE)
+$                           JGS_TERMINATE_DIFFERENCE  : Terminate based on the total change of the unweightet sum of wave action (TRUE/FALSE, default TRUE)
+$                           JGS_TERMINATE_NORM  : Terminate based on the norm of the solution (TRUE/FALSE, default FALSE)
+$                           JGS_USE_JACOBI  : Use Jacobi solver family (TRUE/FALSE, default TRUE)
+$                           JGS_BLOCK_GAUSS_SEIDEL  : Use Block Gauss Seidel method for imptotal instead of the conservative jacobi iterator. (TRUE/FALSE, default TRUE)
+$                           JGS_MAXITER  : Max. Number of solver iterations for JGS_TERMINATE_MAXITER (integer, default 100) 
+$                           JGS_PMIN  : % of grid points that do not need to converge during solver iteration (real, default 1) 
+$                           JGS_DIFF_THR  : Implicit solver threshold for JGS_TERMINATE_DIFFERENCE (real, default 1.0e-10)
+$                           JGS_NORM_THR  : Norm of the solution for JGS_TERMINATE_NORM (real, default 1.0e-20)
+$                           JGS_LIMITER  : TRUE: Use total (quasi-steady: limits whole equation) instead of local limiter (un-steady: limits only source terms)
+$                                          FALSE: default 
+$                           JGS_LIMITER_FUNC  : 1 - old limiter (default)
+$                                               2 - alternatnive limiter
+$                           SETUP_APPLY_WLV  : Compute wave setup (TRUE/FALSE, default TRUE) 
+$                           SOLVERTHR_SETUP  : Solver threshold for setup computations (default 1E-6)
+$                           CRIT_DEP_SETUP  : Critical depth for setup computations (default 0.1) 
 
 $
 $ SMC grid propagation    : Namelist PSMC and default values

model/src/w3iorsmd.F90

@@ -686,6 +686,7 @@ SUBROUTINE W3IORS ( INXOUT, NDSR, DUMFPI, IMOD, FLRSTRT )
         ! Original non-server version writing of spectra
         !
         IF ( .NOT.IOSFLG .OR. (NAPROC.EQ.1.AND.NAPRST.EQ.1) ) THEN
+#ifdef W3_MPI 
           DO JSEA=1, NSEAL
             CALL INIT_GET_ISEA(ISEA, JSEA)
             NREC   = ISEA + 2
@@ -694,6 +695,16 @@ SUBROUTINE W3IORS ( INXOUT, NDSR, DUMFPI, IMOD, FLRSTRT )
             WRITEBUFF(1:NSPEC) = VA(1:NSPEC,JSEA)
             WRITE (NDSR,POS=RPOS,ERR=803,IOSTAT=IERR) WRITEBUFF
           END DO
+#else 
+          DO JSEA=1, NSEA
+            ISEA = JSEA
+            NREC   = ISEA + 2
+            RPOS  = 1_8 + LRECL*(NREC-1_8)
+            WRITEBUFF(:) = 0.
+            WRITEBUFF(1:NSPEC) = VA(1:NSPEC,JSEA)
+            WRITE (NDSR,POS=RPOS,ERR=803,IOSTAT=IERR) WRITEBUFF
+          END DO
+#endif          
           !
           ! I/O server version writing of spectra ( !/MPI )
           !
@@ -843,7 +854,7 @@ SUBROUTINE W3IORS ( INXOUT, NDSR, DUMFPI, IMOD, FLRSTRT )
           ELSE
 #endif
             VA = 0.
-            DO JSEA=1, NSEAL
+            DO JSEA=1, NSEA
               CALL INIT_GET_ISEA(ISEA, JSEA)
               NREC   = ISEA + 2
               RPOS   = 1_8 + LRECL*(NREC-1_8)

model/src/w3ounfmetamd.F90

@@ -2638,8 +2638,8 @@ SUBROUTINE DEFAULT_META()
     !META(1)%VARNS='air_sea_temperature_difference'
     META(1)%VARNS=''
     META(1)%VARNG='air_sea_temperature_difference'
-    META(1)%VMIN = 0
-    META(1)%VMAX = 400
+    META(1)%VMIN = -200.0
+    META(1)%VMAX = 200.0
     ! IFI=1, IFJ=5, WLV
     META => GROUP(1)%FIELD(5)%META
     META(1)%FSC    = 0.01

model/src/w3profsmd.F90

@@ -681,7 +681,7 @@ SUBROUTINE W3XYPFSN2 ( ISP, C, LCALC, RD10, RD20, DT, AC)
         IF (REFPARS(3).LT.0.5.AND.IOBPD(ITH,IP).EQ.0.AND.IOBPA(IP).EQ.0) THEN
           U(IP) = AC(IP) ! restores reflected boundary values
         ENDIF
-#endif^
+#endif
       END DO
       ! update spectrum
       AC = U
@@ -1266,7 +1266,7 @@ SUBROUTINE W3XYPFSNIMP ( ISP, C, LCALC, RD10, RD20, DT, AC)
       DO IBI=1, NBI
         IP    = MAPSF(ISBPI(IBI),1)
         AC(IP) = ( RD1*BBPI0(ISP,IBI) + RD2*BBPIN(ISP,IBI) )   &
-             *IOBPA(IP)*(1-IOBPD(ITH,IP)) / CG(IK,ISBPI(IBI)) * CLATS(ISBPI(IBI))
+             *IOBPA(IP)*IOBPD(ITH,IP) / CG(IK,ISBPI(IBI)) * CLATS(ISBPI(IBI))
       END DO
     END IF
 

model/src/w3profsmd_pdlib.F90

@@ -3642,8 +3642,8 @@ SUBROUTINE calcARRAY_JACOBI_VEC(DTG,FACX,FACY,VGX,VGY)
     DTK    = 0
     TMP3   = 0
 
-    CCOSA = FACX * ECOS
-    CSINA = FACX * ESIN
+    CCOSA = FACX * ECOS(1:NTH)
+    CSINA = FACX * ESIN(1:NTH)
     call print_memcheck(memunit, 'memcheck_____:'//' WW3_JACOBI SECTION 0')
 
     DO ISP = 1, NSPEC

model/src/w3src4md.F90

@@ -666,8 +666,16 @@ SUBROUTINE W3SIN4 (A, CG, K, U, USTAR, DRAT, AS, USDIR, Z0, CD,    &
     ! I got it from, maybe just made up from drag law ...
     !
 #ifdef W3_STAB3
-    Usigma=MAX(0.,-0.025*AS)
+    IF ( ISNAN(AS) ) THEN
+      ! AS is typically NaN on land and can propagate into the domain by interpolation
+      Usigma = 0.
+    ELSE
+      Usigma = MAX(0.,-0.025*AS)
+    END IF
     USTARsigma=(1.0+U/(10.+U))*Usigma
+#endif
+#ifdef W3_T
+    WRITE (NDST,9003) AS, Usigma, USTARsigma, U
 #endif
     UST=USTAR
     ISTAB=3
@@ -678,6 +686,9 @@ SUBROUTINE W3SIN4 (A, CG, K, U, USTAR, DRAT, AS, USDIR, Z0, CD,    &
 #endif
       TAUX = UST**2* COS(USDIR)
       TAUY = UST**2* SIN(USDIR)
+#ifdef W3_T
+      WRITE (NDST,9001) ISTAB, TAUX, TAUY, UST
+#endif
       !
       ! Loop over the resolved part of the spectrum
       !
@@ -788,6 +799,9 @@ SUBROUTINE W3SIN4 (A, CG, K, U, USTAR, DRAT, AS, USDIR, Z0, CD,    &
     YSTRESS=0.5*(STRESSSTAB(1,2)+STRESSSTAB(2,2))
     TAUWNX=0.5*(STRESSSTABN(1,1)+STRESSSTABN(2,1))
     TAUWNY=0.5*(STRESSSTABN(1,2)+STRESSSTABN(2,2))
+#endif
+#ifdef W3_T
+    WRITE (NDST,9002) SUM(D), SUM(A), XSTRESS, YSTRESS, TAUWNX, TAUWNY
 #endif
     S = D * A
     !
@@ -868,6 +882,21 @@ SUBROUTINE W3SIN4 (A, CG, K, U, USTAR, DRAT, AS, USDIR, Z0, CD,    &
     !
 #ifdef W3_T
 9000 FORMAT (' TEST W3SIN4 : COMMON FACT.: ',3E10.3)
+9001 FORMAT (' TEST W3SIN4 : ISTAB      :',I2/                    &
+             '               TAUX       :',E12.3/                 &
+             '               TAUY       :',E12.3/                 &
+             '               UST        :',E12.3)
+9002 FORMAT (' TEST W3SIN4 : SUM(D)     :',E12.3/                 &
+             '               SUM(A)     :',E12.3/                 &
+             '               STRESSX    :',E12.3/                 &
+             '               STRESSY    :',E12.3/                 &
+             '               TAUWNX     :',E12.3/                 &
+             '               TAUWNY     :',E12.3)
+9003 FORMAT (' TEST W3SIN4 : AS         :',F8.4/                  &
+             '               Usigma     :',E12.3/                 &
+             '               USTARsigma :',E12.3/                 &
+             '               U          :',E12.3)
+
 #endif
     !/
     !/ End of W3SIN4 ----------------------------------------------------- /

model/src/w3srcemd.F90

@@ -1424,7 +1424,7 @@ SUBROUTINE W3SRCE ( srce_call, IT, ISEA, JSEA, IX, IY, IMOD,          &
 #ifdef W3_PDLIB
       IF (B_JGS_LIMITER_FUNC == 2) THEN
         DO IK=1, NK
-          JAC      = CG1(IK)/CLATSL 
+          JAC      = CG1(IK)/CLATSL
           JAC2     = 1./TPI/SIG(IK)
           FRLOCAL  = SIG(IK)*TPIINV
 #ifdef W3_ST6
@@ -1449,7 +1449,7 @@ SUBROUTINE W3SRCE ( srce_call, IT, ISEA, JSEA, IX, IY, IMOD,          &
 #ifdef W3_ST6
         VS(IS) = VS(IS) + VSWL(IS)
 #endif
-#ifndef W3_PDLIB 
+#ifndef W3_PDLIB
 #ifdef W3_TR1
         VS(IS) = VS(IS) + VSTR(IS)
 #endif
@@ -1491,8 +1491,8 @@ SUBROUTINE W3SRCE ( srce_call, IT, ISEA, JSEA, IX, IY, IMOD,          &
 #endif
       END DO  ! end of loop on IS
 
-      !VD = 0 
-      !VS = 0 
+      !VD = 0
+      !VS = 0
       !
       DT     = MAX ( 0.5, DT ) ! The hardcoded min. dt is a problem for certain cases e.g. laborotary scale problems.
       !
@@ -1702,7 +1702,8 @@ SUBROUTINE W3SRCE ( srce_call, IT, ISEA, JSEA, IX, IY, IMOD,          &
         RETURN ! return everything is done for the implicit ...
 
       END IF ! srce_imp_pre
-#endif !W3_PDLIB
+!W3_PDLIB
+#endif
       !
 #ifdef W3_T
       WRITE (NDST,9040) DTRAW, DT, SHAVE
@@ -1736,7 +1737,7 @@ SUBROUTINE W3SRCE ( srce_call, IT, ISEA, JSEA, IX, IY, IMOD,          &
           eInc1 = VDTR(IS) * DT / MAX ( 1. , (1.-HDT*VDTR(IS)))
           SPEC(IS) = MAX ( 0. , SPEC(IS)+eInc1 )
         END DO
-#endif 
+#endif
 
 #ifdef W3_DEBUGSRC
         IF (IX == DEBUG_NODE) WRITE(44,'(1EN15.4)') SUM(VSIN)
@@ -2257,7 +2258,7 @@ SUBROUTINE W3SRCE ( srce_call, IT, ISEA, JSEA, IX, IY, IMOD,          &
     IF (IX .eq. DEBUG_NODE) THEN
       WRITE(740+IAPROC,*) '5 : sum(SPEC)=', sum(SPEC)
     END IF
-#endif 
+#endif
 
 #ifdef W3_REF1
     IF (REFLEC(1).GT.0.OR.REFLEC(2).GT.0.OR.(REFLEC(4).GT.0.AND.BERG.GT.0)) THEN

model/src/ww3_ounp.F90

@@ -3356,7 +3356,7 @@ SUBROUTINE W3CRNC (ITYPE, OTYPE, NCTYPE, NCFILE, NCID, DIMID, DIMLN, VARID, ONE,
       IRET=NF90_PUT_ATT(NCID,VARID(12),'scale_factor',1.)
       IRET=NF90_PUT_ATT(NCID,VARID(12),'add_offset',0.)
       IRET=NF90_PUT_ATT(NCID,VARID(12),'valid_min',0.)
-      IRET=NF90_PUT_ATT(NCID,VARID(12),'valid_max',100.)
+      IRET=NF90_PUT_ATT(NCID,VARID(12),'valid_max',1000.)
       IRET=NF90_PUT_ATT(NCID,VARID(12),'_FillValue',NF90_FILL_FLOAT)
       IRET=NF90_PUT_ATT(NCID,VARID(12),'content','TXY')
       IRET=NF90_PUT_ATT(NCID,VARID(12),'associates','time station frequency')

model/src/ww3_prnc.F90

@@ -299,7 +299,8 @@ PROGRAM W3PRNC
   REAL, ALLOCATABLE       :: XC(:,:), YC(:,:), AC(:,:),           &
        DATA(:,:), XTEMP(:,:)
   !
-  REAL, POINTER           :: ALA(:,:), ALO(:,:)
+  REAL, ALLOCATABLE, TARGET :: ALA(:,:), ALO(:,:)
+  REAL, POINTER           :: PTR_ALA(:,:), PTR_ALO(:,:)
   !
   DOUBLE PRECISION        :: REFJULDAY, CURJULDAY, STARTJULDAY, STPJULDAY
   !
@@ -1007,7 +1008,9 @@ PROGRAM W3PRNC
       !
       ! ... create grid search utility
       !
-      GSI = W3GSUC( .TRUE., FLAGLL, ICLO, ALO, ALA )
+      PTR_ALA => ALA
+      PTR_ALO => ALO
+      GSI = W3GSUC( .TRUE., FLAGLL, ICLO, PTR_ALO, PTR_ALA )
       !
       ! ... construct Interpolation data
       !
@@ -1210,9 +1213,9 @@ PROGRAM W3PRNC
         !
         ! ... read lat-lon data
         !
-        IF ( ASSOCIATED(ALA) ) THEN
+        IF ( ALLOCATED(ALA) ) THEN
           DEALLOCATE ( ALA, ALO )
-          NULLIFY ( ALA, ALO )
+          NULLIFY ( PTR_ALA, PTR_ALO )
         END IF
         ALLOCATE ( ALA(NXJ(J),NYJ(J)), ALO(NXJ(J),NYJ(J)) )
         CALL INA2R (ALA, NXJ(J), NYJ(J), 1, NXJ(J), 1, NYJ(J),&
@@ -2221,7 +2224,7 @@ PROGRAM W3PRNC
   END DO ! NTI
   !
   DEALLOCATE(XC,YC,AC,XTEMP)
-  IF (ASSOCIATED(ALA)) DEALLOCATE(ALA,ALO)
+  IF (ALLOCATED(ALA)) DEALLOCATE(ALA,ALO)
   !
   !     End loop over input fields
   !--- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -