--- MITgcm/pkg/ptracers/ptracers_integrate.F	2004/10/28 00:33:56	1.19
+++ MITgcm/pkg/ptracers/ptracers_integrate.F	2005/10/10 05:53:48	1.25
@@ -1,12 +1,7 @@
-C $Header: /home/ubuntu/mnt/e9_copy/MITgcm/pkg/ptracers/ptracers_integrate.F,v 1.19 2004/10/28 00:33:56 jmc Exp $
+C $Header: /home/ubuntu/mnt/e9_copy/MITgcm/pkg/ptracers/ptracers_integrate.F,v 1.25 2005/10/10 05:53:48 mlosch Exp $
 C $Name:  $
 
 #include "PTRACERS_OPTIONS.h"
-cswdptr -- add ---
-#ifdef ALLOW_GCHEM
-# include "GCHEM_OPTIONS.h"
-#endif
-cswdptr -- end add ---
 
 CBOP
 C !ROUTINE: PTRACERS_INTEGRATE
@@ -78,6 +73,7 @@
       INTEGER kUp,kDown,km1
       INTEGER GAD_TR
       LOGICAL calcAdvection
+      INTEGER iterNb
 CEOP
 
 C Loop over tracers
@@ -111,65 +107,48 @@
      I                   GAD_TR,
      I                   PTRACERS_advScheme(iTracer),
      I                   PTRACERS_advScheme(iTracer),
-     I                   calcAdvection, .FALSE.,
+     I                   calcAdvection, PTRACERS_ImplVertAdv(iTracer),
      U                   rFlx(1-Olx,1-Oly,1,iTracer),
      U                   gPtr(1-Olx,1-Oly,1,1,1,iTracer),
      I                   myTime, myIter, myThid )
 
 C External forcing term(s)
-cswdptr --add --
-#ifdef ALLOW_GCHEM
-#ifndef PTRACERS_SEPARATE_FORCING
-       IF ( forcing_In_AB )
-     &    CALL GCHEM_FORCING_INT(
-     I                        bi,bj,iMin,iMax,jMin,jMax,k,
-     I                        iTracer,
-     I                        myTime,myIter, myThid)
-#endif
-#else
-cswdptr - end add ---
        IF ( forcing_In_AB )
      &   CALL PTRACERS_FORCING(
-     I                      bi,bj,iMin,iMax,jMin,jMax,k,
+     I                      bi,bj,iMin,iMax,jMin,jMax,k,iTracer,
      U                      gPtr(1-Olx,1-Oly,1,1,1,iTracer),
      I                      surfaceForcingPtr(1-Olx,1-Oly,1,1,iTracer),
      I                      myIter,myTime,myThid)
-cswdptr --add---
-#endif
-cswdptr -- end add ---
 
 C If using Adams-Bashforth II, then extrapolate tendancies
+C gPtr is now the tracer tendency for explicit advection/diffusion
       IF ( PTRACERS_advScheme(iTracer).EQ.ENUM_CENTERED_2ND
      & .OR.PTRACERS_advScheme(iTracer).EQ.ENUM_UPWIND_3RD
      & .OR.PTRACERS_advScheme(iTracer).EQ.ENUM_CENTERED_4TH ) THEN
+#ifdef ALLOW_MATRIX
+C  If matrix is being computed, block call to S/R ADAMS_BASHFORTH2 to 
+C  prevent gPtr from being replaced by the average of gPtr and gPtrNm1.    
+        IF (.NOT.useMATRIX) THEN
+#endif          
+        iterNb = myIter
+        IF (staggerTimeStep) iterNb = myIter - 1
         CALL ADAMS_BASHFORTH2(
      I                        bi,bj,K,
      U                        gPtr(1-Olx,1-Oly,1,1,1,iTracer),
      U                        gPtrNm1(1-Olx,1-Oly,1,1,1,iTracer),
-     I                        myIter,myThid )
+     I                        iterNb, myThid )
+#ifdef ALLOW_MATRIX
+        ENDIF
+#endif     
       ENDIF
 
 C External forcing term(s)
-cswdptr - add--
-#ifdef ALLOW_GCHEM
-#ifndef PTRACERS_SEPARATE_FORCING
-       IF ( .NOT.forcing_In_AB )
-     &    CALL GCHEM_FORCING_INT(
-     I                        bi,bj,iMin,iMax,jMin,jMax,k,
-     I                        iTracer,
-     I                        myTime,myIter, myThid)
-#endif
-#else
-cswdptr - end add ---
        IF ( .NOT.forcing_In_AB )
      &   CALL PTRACERS_FORCING(
-     I                      bi,bj,iMin,iMax,jMin,jMax,k,
+     I                      bi,bj,iMin,iMax,jMin,jMax,k,iTracer,
      U                      gPtr(1-Olx,1-Oly,1,1,1,iTracer),
      I                      surfaceForcingPtr(1-Olx,1-Oly,1,1,iTracer),
      I                      myIter,myTime,myThid)
-cswdptr - add--
-#endif
-cswdptr -- end add ---
 
 #ifdef NONLIN_FRSURF
 C Account for change in level thickness
@@ -196,6 +175,15 @@
      I                        gPtr(1-Olx,1-Oly,1,1,1,iTracer),
      I                        myIter,myThid )
 
+#ifdef   ALLOW_OBCS
+C Apply open boundary conditions
+         IF (useOBCS) THEN
+          CALL OBCS_APPLY_PTRACER( 
+     I         bi, bj, k, iTracer, 
+     U         gPtr(1-Olx,1-Oly,k,bi,bj,iTracer),
+     I         myThid )
+         END IF
+#endif   /* ALLOW_OBCS */
 C end of tracer loop
       ENDDO