<p><b>mpetersen@lanl.gov</b> 2010-11-15 14:53:50 -0700 (Mon, 15 Nov 2010)</p><p>BRANCH COMMIT Updating topography branch.  This is the second part of the revisions after Todd's branch review.  This has a bit-for-bit match with the previous commit for z-level runs.<br>
</p><hr noshade><pre><font color="gray">Modified: branches/ocean_projects/topography2_mrp/src/core_ocean/module_time_integration.F
===================================================================
--- branches/ocean_projects/topography2_mrp/src/core_ocean/module_time_integration.F        2010-11-15 20:47:44 UTC (rev 615)
+++ branches/ocean_projects/topography2_mrp/src/core_ocean/module_time_integration.F        2010-11-15 21:53:50 UTC (rev 616)
@@ -498,10 +498,9 @@
 
             do k=1,maxLevelEdgeTop(iEdge)
 
-               u_diffusion = ( divergence(k,cell2)  - divergence(k,cell1) ) / dcEdge(iEdge)  &amp;
-                            -( vorticity(k,vertex2) - vorticity(k,vertex1)) / dvEdge(iEdge)
- 
-               delsq_u(k,iEdge) = delsq_u(k,iEdge) + u_diffusion
+               delsq_u(k,iEdge) = &amp; 
+                  ( divergence(k,cell2)  - divergence(k,cell1) ) / dcEdge(iEdge)  &amp;
+                 -( vorticity(k,vertex2) - vorticity(k,vertex1)) / dvEdge(iEdge)
 
             end do
          end do
@@ -595,6 +594,9 @@
       !
       ! velocity tendency: forcing and bottom drag
       !
+      ! mrp 101115 note: in order to include flux boundary conditions, we will need to 
+      ! know the bottom edge with nonzero velocity and place the drag there.
+
       do iEdge=1,grid % nEdgesSolve
 
         ! forcing in top layer only
@@ -750,6 +752,11 @@
       !
       ! tracer tendency: horizontal advection term -div( h \phi u)
       !
+      ! mrp 101115 note: in order to include flux boundary conditions, we will need to 
+      ! assign h_edge for maxLevelEdgeTop:maxLevelEdgeBot in the compute_solve_diagnostics
+      ! and then change maxLevelEdgeTop to maxLevelEdgeBot in the following section.
+      ! tracer_edge at the boundary will also need to be defined for flux boundaries.
+
       coef_3rd_order = 0.
       if (config_tracer_adv_order == 3) coef_3rd_order = 1.0
       if (config_tracer_adv_order == 3 .and. config_monotonic) coef_3rd_order = 0.25
@@ -1192,6 +1199,8 @@
       ! Compute height on cell edges at velocity locations
       !   Namelist options control the order of accuracy of the reconstructed h_edge value
       !
+      ! mrp 101115 note: in order to include flux boundary conditions, we will need to 
+      ! assign h_edge for maxLevelEdgeTop:maxLevelEdgeBot in the following section
 
       coef_3rd_order = 0.
       if (config_thickness_adv_order == 3) coef_3rd_order = 1.0
@@ -1311,7 +1320,7 @@
       do iEdge=1,nEdges
          vertex1 = verticesOnEdge(1,iEdge)
          vertex2 = verticesOnEdge(2,iEdge)
-         do k=1,maxLevelEdgetop(iEdge)
+         do k=1,maxLevelEdgeBot(iEdge)
             circulation(k,vertex1) = circulation(k,vertex1) - dcEdge(iEdge) * u(k,iEdge)
             circulation(k,vertex2) = circulation(k,vertex2) + dcEdge(iEdge) * u(k,iEdge)
          end do
@@ -1329,7 +1338,7 @@
       do iEdge=1,nEdges
          cell1 = cellsOnEdge(1,iEdge)
          cell2 = cellsOnEdge(2,iEdge)
-         do k=1,maxLevelEdgeTop(iEdge)
+         do k=1,maxLevelEdgeBot(iEdge)
              divergence(k,cell1) = divergence(k,cell1) + u(k,iEdge)*dvEdge(iEdge)
              divergence(k,cell2) = divergence(k,cell2) - u(k,iEdge)*dvEdge(iEdge)
          enddo
@@ -1364,7 +1373,7 @@
       do iEdge = 1,nEdges
          do i=1,nEdgesOnEdge(iEdge)
             eoe = edgesOnEdge(i,iEdge)
-            do k = 1,maxLevelEdgeTop(iEdge)
+            do k = 1,maxLevelEdgeBot(iEdge)
                v(k,iEdge) = v(k,iEdge) + weightsOnEdge(i,iEdge) * u(k, eoe)
             end do
          end do
@@ -1547,7 +1556,7 @@
         do iEdge=1,nEdges
            cell1 = cellsOnEdge(1,iEdge)
            cell2 = cellsOnEdge(2,iEdge)
-           do k=1,maxLevelEdgeTop(iEdge)
+           do k=1,maxLevelEdgeBot(iEdge)
               flux = u(k,iEdge) * dvEdge(iEdge) 
               div_u(k,cell1) = div_u(k,cell1) + flux
               div_u(k,cell2) = div_u(k,cell2) - flux

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