--- MITgcm/model/src/calc_3d_diffusivity.F	2007/09/27 14:42:59	1.12
+++ MITgcm/model/src/calc_3d_diffusivity.F	2011/09/20 22:25:23	1.17
@@ -1,4 +1,4 @@
-C $Header: /home/ubuntu/mnt/e9_copy/MITgcm/model/src/calc_3d_diffusivity.F,v 1.12 2007/09/27 14:42:59 dimitri Exp $
+C $Header: /home/ubuntu/mnt/e9_copy/MITgcm/model/src/calc_3d_diffusivity.F,v 1.17 2011/09/20 22:25:23 jmc Exp $
 C $Name:  $
 
 #include "PACKAGES_CONFIG.h"
@@ -36,7 +36,10 @@
 #endif
 #ifdef ALLOW_PTRACERS
 #include "PTRACERS_SIZE.h"
-#include "PTRACERS.h"
+#include "PTRACERS_PARAMS.h"
+#endif
+#ifdef ALLOW_LONGSTEP
+#include "LONGSTEP.h"
 #endif
 
 C     !INPUT/OUTPUT PARAMETERS:
@@ -82,12 +85,25 @@
 #endif
         DO j = 1-Oly,sNy+Oly
          DO i = 1-Olx,sNx+Olx
-          KappaRTr(i,j,k) =
+#ifdef ALLOW_LONGSTEP
+          IF ( trIdentity .GE. GAD_TR1) THEN
+           KappaRTr(i,j,k) =
+     &         LS_IVDConvCount(i,j,k,bi,bj)*ivdc_kappa
+     &         + KbryanLewis79
+#ifdef ALLOW_BL79_LAT_VARY
+     &         + (KbryanLewisEQ-KbryanLewis79)*BL79LatArray(i,j,bi,bj)
+#endif
+          ELSE
+#else
+          IF ( .TRUE. ) THEN
+#endif /* ALLOW_LONGSTEP */
+           KappaRTr(i,j,k) =
      &         IVDConvCount(i,j,k,bi,bj)*ivdc_kappa
      &         + KbryanLewis79
 #ifdef ALLOW_BL79_LAT_VARY
      &         + (KbryanLewisEQ-KbryanLewis79)*BL79LatArray(i,j,bi,bj)
 #endif
+          ENDIF
          ENDDO
         ENDDO
        ENDDO
@@ -96,8 +112,7 @@
          DO j = 1-Oly,sNy+Oly
           DO i = 1-Olx,sNx+Olx
            KappaRTr(i,j,k) = KappaRTr(i,j,k)
-#if (defined ALLOW_3D_DIFFKR || \
-     (defined (ALLOW_AUTODIFF_TAMC) && defined (ALLOW_DIFFKR_CONTROL)))
+#ifdef ALLOW_3D_DIFFKR
      &          + diffKr(i,j,k,bi,bj)
 #else
      &          + diffKrNrT(k)
@@ -110,8 +125,7 @@
          DO j = 1-Oly, sNy+Oly
           DO i = 1-Olx, sNx+Olx
            KappaRTr(i,j,k) = KappaRTr(i,j,k)
-#if (defined ALLOW_3D_DIFFKR || \
-     (defined (ALLOW_AUTODIFF_TAMC) && defined (ALLOW_DIFFKR_CONTROL)))
+#ifdef ALLOW_3D_DIFFKR
      &          + diffKr(i,j,k,bi,bj)
 #else
      &          + diffKrNrS(k)
@@ -120,16 +134,14 @@
          ENDDO
         ENDDO
 #ifdef ALLOW_PTRACERS
-       ELSEIF ( trIdentity.GE.GAD_TR1
-     &   .AND. trIdentity.LT.GAD_TR1+PTRACERS_numInUse) THEN
+       ELSEIF ( trIdentity.GE.GAD_TR1) THEN
 
         iTr = trIdentity - GAD_TR1 + 1
         DO k = 1,Nr
          DO j = 1-Oly, sNy+Oly
           DO i = 1-Olx, sNx+Olx
            KappaRTr(i,j,k) = KappaRTr(i,j,k)
-#if (defined ALLOW_3D_DIFFKR || \
-     (defined (ALLOW_AUTODIFF_TAMC) && defined (ALLOW_DIFFKR_CONTROL)))
+#ifdef ALLOW_3D_DIFFKR
      &          + diffKr(i,j,k,bi,bj)
 #else
      &          + PTRACERS_diffKrNr(k,iTr)
@@ -156,27 +168,25 @@
      I        bi,bj,iMin,iMax,jMin,jMax,0,Nr,
      O        KappaRTr,
      I        myThid)
-       ELSE
+       ELSEIF (trIdentity.EQ.GAD_SALINITY) THEN
          CALL KPP_CALC_DIFF_S(
      I        bi,bj,iMin,iMax,jMin,jMax,0,Nr,
      O        KappaRTr,
      I        myThid)
+#ifdef ALLOW_PTRACERS
+       ELSEIF ( trIdentity.GE.GAD_TR1) THEN
+         iTr = trIdentity - GAD_TR1 + 1
+         CALL KPP_CALC_DIFF_Ptr(
+     I        bi,bj,iMin,iMax,jMin,jMax,0,Nr,
+     O        KappaRTr,
+     I        iTr, myThid )
+#endif /* ALLOW_PTRACERS */
+       ELSE
+        WRITE(msgBuf,'(A,I4)')
+     &       ' CALC_3D_DIFFUSIVITY: Invalid tracer Id: ',trIdentity
+        CALL PRINT_ERROR( msgBuf, myThid )
+        STOP 'ABNORMAL END: S/R CALC_3D_DIFFUSIVITY'
        ENDIF
-#if (defined ALLOW_PTRACERS && ! (defined ALLOW_3D_DIFFKR || \
-     (defined (ALLOW_AUTODIFF_TAMC) && defined (ALLOW_DIFFKR_CONTROL))))
-       IF ( trIdentity.GE.GAD_TR1
-     &   .AND. trIdentity.LT.GAD_TR1+PTRACERS_numInUse) THEN
-        iTr = trIdentity - GAD_TR1 + 1
-        DO k = 1,Nr
-         DO j = 1-Oly, sNy+Oly
-          DO i = 1-Olx, sNx+Olx
-           KappaRTr(i,j,k) = KappaRTr(i,j,k)
-     &          - diffKrNrS(k) + PTRACERS_diffKrNr(k,iTr)
-          ENDDO
-         ENDDO
-        ENDDO
-       ENDIF
-#endif
       ENDIF
 #endif /* ALLOW_KPP */
 
@@ -185,7 +195,7 @@
          CALL GMREDI_CALC_DIFF(
      I        bi,bj,iMin,iMax,jMin,jMax,0,Nr,
      U        KappaRTr,
-     I        myThid)
+     I        trIdentity,myThid)
       ENDIF
 #endif
 
@@ -217,8 +227,8 @@
 #endif
 
 C-    Apply mask to vertical diffusivity
-C jmc: don't have the impression that masking is needed
-C      but could be removed later if it's the case.
+C jmc: do not have the impression that masking is needed
+C      but could be removed later if it is the case.
 c     DO j = 1-Oly, sNy+Oly
 c      DO i = 1-Olx, sNx+Olx
 c       KappaRTr(i,j,k) = maskUp(i,j)*KappaRTr(i,j,k)