<p><b>dwj07@fsu.edu</b> 2012-03-15 12:59:24 -0600 (Thu, 15 Mar 2012)</p><p><br>
        -- BRANCH COMMIT --<br>
<br>
        Having basin write the dx directory, which is linked to each directory for a given run.<br>
</p><hr noshade><pre><font color="gray">Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/basin_src/basin-template.F
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/basin_src/basin-template.F        2012-03-15 17:18:06 UTC (rev 1648)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/basin_src/basin-template.F        2012-03-15 18:59:24 UTC (rev 1649)
@@ -215,31 +215,31 @@
 ! write OpenDx file
 !write(6,*) ' calling write_OpenDX'
 !write(6,*)
-!call write_OpenDX(           on_a_sphere, &amp;
-!                             nCellsNew, &amp;
-!                             nVerticesNew, &amp;
-!                             nEdgesNew, &amp;
-!                             vertexDegreeNew, &amp;
-!                             maxEdgesNew, &amp;
-!                             xCellNew, &amp;
-!                             yCellNew, &amp;
-!                             zCellNew, &amp;
-!                             xVertexNew, &amp;
-!                             yVertexNew, &amp;
-!                             zVertexNew, &amp;
-!                             xEdgeNew, &amp;
-!                             yEdgeNew, &amp;
-!                             zEdgeNew, &amp;
-!                             nEdgesOnCellNew, &amp;
-!                             verticesOnCellNew, &amp;
-!                             verticesOnEdgeNew, &amp;
-!                             cellsOnVertexNew, &amp;
-!                             edgesOnCellNew, &amp;
-!                             areaCellNew, &amp;
-!                             maxLevelCellNew, &amp;
-!                             depthCell, &amp;
-!                             temperatureNew(1,1,:), &amp;
-!                             kiteAreasOnVertexNew )
+ call write_OpenDX(           on_a_sphere, &amp;
+                              nCellsNew, &amp;
+                              nVerticesNew, &amp;
+                              nEdgesNew, &amp;
+                              vertexDegreeNew, &amp;
+                              maxEdgesNew, &amp;
+                              xCellNew, &amp;
+                              yCellNew, &amp;
+                              zCellNew, &amp;
+                              xVertexNew, &amp;
+                              yVertexNew, &amp;
+                              zVertexNew, &amp;
+                              xEdgeNew, &amp;
+                              yEdgeNew, &amp;
+                              zEdgeNew, &amp;
+                              nEdgesOnCellNew, &amp;
+                              verticesOnCellNew, &amp;
+                              verticesOnEdgeNew, &amp;
+                              cellsOnVertexNew, &amp;
+                              edgesOnCellNew, &amp;
+                              areaCellNew, &amp;
+                              maxLevelCellNew, &amp;
+                              depthCell, &amp;
+                              temperatureNew(1,1,:), &amp;
+                              kiteAreasOnVertexNew )
 
 
 !do iCell=1,nCellsNew

Deleted: branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/basin_src/basin.F
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/basin_src/basin.F        2012-03-15 17:18:06 UTC (rev 1648)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/basin_src/basin.F        2012-03-15 18:59:24 UTC (rev 1649)
@@ -1,1626 +0,0 @@
-program map_to_basin
-
-use read_netcdf
-use read_topo
-use read_TS
-use write_netcdf
-use utilities
-use cullLoops
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-! Program: basin.F
-!
-! This program is meant to add land to grids, as well as initial conditions.
-! 
-! This program is used to take a specific mesh, and remove Cells from it
-! It can be used to change a planar grid into a Channel or a basin grid, or to 
-! Change a spherical grid into a Limited area spherical grid.
-!
-! How to use:
-! Step 1: Set the number of Vertical levels
-! Step 2: Set if the grid is on a sphere or not, and it's radius
-! Step 3: Specify some Parameters
-! Step 4: Check the Initial conditions routine get_init_conditions
-! Step 5: Check the depth routine define_kmt
-!
-!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-implicit none
-
-integer, parameter :: nx = 50
-! This needs to be changed for correct periodic boundaries
-! Lx is the TOTAL domain width, and needs to be exact for correct periodic
-! boundaries in x.
-real, parameter :: Lx = 160.0e3
-
-! original grid variables
-integer :: time, nCells, nEdges, nVertices
-integer :: maxEdges, maxEdges2, TWO, vertexDegree, nVertLevels
-integer, allocatable, dimension(:) :: indexToCellID, indexToEdgeID, indexToVertexID
-real, allocatable, dimension(:) :: xCell, yCell, zCell, latCell, lonCell, meshDensity
-real, allocatable, dimension(:) :: xEdge, yEdge, zEdge, latEdge, lonEdge
-real, allocatable, dimension(:) :: xVertex, yVertex, zVertex, latVertex, lonVertex
-integer, allocatable, dimension(:) :: nEdgesOnCell, nEdgesOnEdge
-integer, allocatable, dimension(:,:) :: cellsOnCell, edgesOnCell, verticesOnCell
-integer, allocatable, dimension(:,:) :: cellsOnEdge, verticesOnEdge, edgesOnEdge
-integer, allocatable, dimension(:,:) :: cellsOnVertex, edgesOnVertex
-real, allocatable, dimension(:) :: areaCell, areaTriangle, dcEdge, dvEdge, angleEdge
-real, allocatable, dimension(:,:) :: kiteAreasOnVertex, weightsOnEdge
-
-real, allocatable, dimension(:) :: fEdge, fVertex, h_s, work1
-real, allocatable, dimension(:,:) :: u_src
-real, allocatable, dimension(:,:,:) :: u, v, h
-real, allocatable, dimension(:,:,:) :: rho
-
-integer nlon, nlat, ndepth
-real(kind=4), allocatable, dimension(:) :: t_lon, t_lat, depth_t
-real(kind=4), allocatable, dimension(:,:) :: mTEMP, mSALT
-real(kind=4), allocatable, dimension(:,:,:) :: TEMP, SALT
-real(kind=4), allocatable, dimension(:,:) :: TAUX, TAUY
-
-real, dimension(40) :: dz
-
-! Step 1: Set the number of Vertical levels
-integer, parameter :: nVertLevelsMOD = 20
-
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-! basin-mod
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-!
-! Need to uncomment the options appropriate for the input grid file. If it's on
-! a sphere, specify the flag &quot;on_a_sphere&quot; and &quot;sphere_radius&quot;. Otherwise set
-! them equal to NO and 0.0 respectively
-!
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-
-
-! Step 2: Set if the grid is on a sphere or not, and it's radius
-!character (len=16) :: on_a_sphere = 'YES              '
-!real*8, parameter :: sphere_radius = 6.37122e6
-!real*8, parameter :: sphere_radius = 1.0
-
-character (len=16) :: on_a_sphere = 'NO               '
-real*8, parameter :: sphere_radius = 0.0
-
-logical, parameter :: real_bathymetry=.false.
-logical, parameter :: eliminate_inland_seas=.false.
-logical, parameter :: l_woce = .false.
-
-
-! Step 3: Specify some Parameters
-   real (kind=8), parameter :: &amp;
-    h_total_max = 1000.0, &amp;
-    u_max = 0.0, &amp;
-    u_src_max = 0.0, &amp; ! max wind stress, N/m2
-    beta = 0.0, &amp;
-    f0 = 1.2e-4, &amp;
-    omega = 0.0
-
-   real (kind=8) :: ymid, ytmp, ymax, xmid, xloc, yloc, pert, ymin, distance, r, c1(3), c2(3)
-   real (kind=8) :: latmid, lattmp, latmax, latmin
-   integer :: cell1, cell2
-
-
-! new grid variables
-integer :: nCellsNew, nEdgesNew, nVerticesNew
-integer :: maxEdgesNew, maxEdges2New, TWONew, vertexDegreeNew, nVertLevelsNew
-integer, allocatable, dimension(:) :: indexToCellIDNew, indexToEdgeIDNew, indexToVertexIDNew
-real, allocatable, dimension(:) :: xCellNew, yCellNew, zCellNew, latCellNew, lonCellNew, meshDensityNew
-real, allocatable, dimension(:) :: xEdgeNew, yEdgeNew, zEdgeNew, latEdgeNew, lonEdgeNew
-real, allocatable, dimension(:) :: xVertexNew, yVertexNew, zVertexNew, latVertexNew, lonVertexNew
-integer, allocatable, dimension(:) :: nEdgesOnCellNew, nEdgesOnEdgeNew, flipVerticesOnEdgeOrdering
-integer, allocatable, dimension(:,:) :: cellsOnCellNew, edgesOnCellNew, verticesOnCellNew
-integer, allocatable, dimension(:,:) :: cellsOnEdgeNew, verticesOnEdgeNew, edgesOnEdgeNew
-integer, allocatable, dimension(:,:) :: cellsOnVertexNew, edgesOnVertexNew
-integer, allocatable, dimension(:,:) :: boundaryEdgeNew, boundaryVertexNew
-real, allocatable, dimension(:) :: areaCellNew, areaTriangleNew, dcEdgeNew, dvEdgeNew, angleEdgeNew
-real, allocatable, dimension(:,:) :: kiteAreasOnVertexNew, weightsOnEdgeNew, normalsNew
-
-real, allocatable, dimension(:) :: fEdgeNew, fVertexNew, h_sNew, hZLevel
-real, allocatable, dimension(:,:) :: u_srcNew
-real, allocatable, dimension(:,:,:) :: uNew, vNew, hNew
-real, allocatable, dimension(:,:,:) :: rhoNew, temperatureNew, salinityNew, tracer1New
-real, allocatable, dimension(:) :: temperatureRestoreNew, salinityRestoreNew
-
-! mapping variables
-integer, allocatable, dimension(:) :: kmt, maxLevelCellNew
-integer, allocatable, dimension(:) :: cellMap, edgeMap, vertexMap
-real, allocatable, dimension(:) :: depthCell
-
-! work variables
-integer :: i,j,jNew,k,jEdge,jEdgeNew,iVertex1New,iVertex2New,iCell1New,iCell2New
-integer :: iCell, iCell1, iCell2, iCell3, iEdge, iVertex, iVertex1, iVertex2
-integer :: iCellNew, iEdgeNew, iVertexNew, ndata, jCell1, jCell2, jCell, iter
-real :: xin, yin, zin, ulon, ulat, ux, uy, uz, rlon, rlat, temp_t, temp_s
-
-! get to work
-write(6,*) ' starting'
-write(6,*)
-
-! get depth profile for later
-!call get_dz
-
-! get grid
-write(6,*) ' calling read_grid'
-write(6,*)
-call read_grid
-write(6,*) ' xCell 1: ',minval(xCell), maxval(xCell)
-
-! copy dimensions
-write(6,*) ' copy dimensions'
-write(6,*)
-call copy_dimensions
-write(6,*) ' xCell 1: ',minval(xCell), maxval(xCell)
-
-! define the kmt array
-write(6,*) ' calling define_kmt'
-write(6,*)
-call define_kmt
-
-! define the mapping between original and new cells, edges and vertices
-write(6,*) ' calling define_mapping'
-write(6,*)
-call define_mapping
-
-! copy the vector arrays form the original to new arrays
-write(6,*) ' calling map_vectors'
-write(6,*)
-call map_vectors
-
-! define the new connectivity variables
-write(6,*) ' calling map_connectivity'
-write(6,*)
-call map_connectivity
-
-! check the mesh
-call error_checking
-
-!write(6,*) ' getting woce t and s '
-!call read_TS_init(nlon, nlat, ndepth)
-!write(6,*) ' TS INIT ', nlon, nlat, ndepth
-!allocate(t_lon(nlon), t_lat(nlat), depth_t(ndepth), TEMP(nlon,nlat,ndepth), SALT(nlon,nlat,ndepth))
-!allocate(TAUX(nlon,nlat), TAUY(nlon,nlat))
-!allocate(mTEMP(nlat,ndepth), mSALT(nlat,ndepth))
-!call read_TS_fields(t_lon, t_lat, depth_t, TEMP, SALT, TAUX, TAUY)
-!call read_TS_finalize()
-!do k=1,ndepth
-!     ndata = 0; temp_t=0; temp_s=0
-!     do j=1,nlat
-!     do i=1,nlon
-!       if(TEMP(i,j,k).gt.-10.0) then
-!         ndata = ndata + 1
-!         temp_t = temp_t + TEMP(i,j,k)
-!         temp_s = temp_s + SALT(i,j,k)
-!       endif
-!     enddo
-!     enddo
-!     mTEMP(:,k) = temp_t / float(ndata)
-!     mSALT(:,k) = temp_s / float(ndata)
-!     write(6,*) ndata,mTemp(1,k),mSalt(1,k)
-!enddo
-
-! generate initial conditions
-call get_init_conditions
-
-! dump new grid to netCDF
-write(6,*) ' calling write_grid'
-write(6,*)
-call write_grid
-
-! dump graph for partioning
-write(6,*) ' call write_graph'
-write(6,*)
-call write_graph
-
-! write OpenDx file
-!write(6,*) ' calling write_OpenDX'
-!write(6,*)
-!call write_OpenDX(           on_a_sphere, &amp;
-!                             nCellsNew, &amp;
-!                             nVerticesNew, &amp;
-!                             nEdgesNew, &amp;
-!                             vertexDegreeNew, &amp;
-!                             maxEdgesNew, &amp;
-!                             xCellNew, &amp;
-!                             yCellNew, &amp;
-!                             zCellNew, &amp;
-!                             xVertexNew, &amp;
-!                             yVertexNew, &amp;
-!                             zVertexNew, &amp;
-!                             xEdgeNew, &amp;
-!                             yEdgeNew, &amp;
-!                             zEdgeNew, &amp;
-!                             nEdgesOnCellNew, &amp;
-!                             verticesOnCellNew, &amp;
-!                             verticesOnEdgeNew, &amp;
-!                             cellsOnVertexNew, &amp;
-!                             edgesOnCellNew, &amp;
-!                             areaCellNew, &amp;
-!                             maxLevelCellNew, &amp;
-!                             depthCell, &amp;
-!                             temperatureNew(1,1,:), &amp;
-!                             kiteAreasOnVertexNew )
-
-
-!do iCell=1,nCellsNew
-  !ulon = 1.0; ulat = 0.0
-  !xin = xCellNew(iCell); yin = yCellNew(iCell); zin = zCellNew(iCell)
-  !call transform_from_lonlat_to_xyz(xin, yin, zin, ulon, ulat, ux, uy, uz)
-  !if(abs(ux).lt.1.0e-10) ux=0.0
-  !if(abs(uy).lt.1.0e-10) uy=0.0
-  !if(abs(uz).lt.1.0e-10) uz=0.0
-  !write(20,10) ux, uy, uz
-  !10 format(3e25.10)
-!enddo
-  
-write(6,*) ' finished'
-
-contains
-
-subroutine write_graph
-implicit none
-integer :: m,itmp(maxEdgesNew),k
-
-      m=nEdgesNew
-      do i=1,nCellsNew
-      do j=1,nEdgesOnCellNew(i)
-         if(cellsOnCellNew(j,i).eq.0) m=m-1
-      enddo
-      enddo
-
-      open(42,file='graph.info',form='formatted')
-      write(42,*) nCellsNew, m
-      do i=1,nCellsNew
-         itmp = 0; k = 0;
-         do j=1,nEdgesOnCellNew(i)
-            if(cellsOnCellNew(j,i).gt.0) then
-              k=k+1; itmp(k)=cellsOnCellNew(j,i)
-            endif
-         enddo
-         write(42,'(1x,12i8)',advance='no') (itmp(m),m=1,k)
-         write(42,'(1x)')
-      end do
-      close(42)
-end subroutine write_graph
-
-
-!Step 4: Check the Initial conditions routine get_init_conditions
-subroutine get_init_conditions
-implicit none
-real :: halfwidth, dtr, pi, p(3), q(3), xin, yin, zin, ulon, ulat, stress, n1, n2, distance, r, temp_t, temp_s
-real :: dotProd
-real :: surfMaxTemp, surfMinTemp
-real :: y_0, x_0, x_1, x_2, x_3, width, cff1
-real :: yTrans, vertTempChange, maxTemp
-real, dimension(:,:,:), allocatable :: tempHolder
-integer :: iTracer, ix, iy, ndata, i, j, k, ixt, iyt, ncull, jcount, iNoData, kdata(nVertLevelsMod)
-logical :: flag_lat
-
-pi = 4.0*atan(1.0)
-dtr = pi/180.0
-
-hNew = 100.0
-temperatureNew = 1.0
-salinityNew = 1.0
-tracer1New = 1.0
-uNew = 0
-vNew = 0
-
-allocate(tempHolder(1, nVertLevelsMOD, nCellsNew))
-
-if(.not.real_bathymetry) then
-
-   write(6,*) ' not using real bathymetry'
-
-   fEdgeNew(:) = 0.0
-   fVertexNew(:) = 0.0
-   h_sNew(:) = 0.0
-   uNew(:,:,:) = 0.0
-   vNew(:,:,:) = 0.0
-
- ! basin-mod
- ! setting for three levels - Set h values for isopycnal system
-   write(6,*) ' setting three levels for isopycnal system'
-   do i = 1, nVertLevelsMOD
-       hNew(1,i,:) = i * h_total_max / nVertLevelsMOD
-       hZLevel(i) =  i * h_total_max / nVertLevelsMOD
-   end do
-
-   h_sNew(:) = -h_total_max
-
-   ! basin-mod
-   !Specify Density values for isopycnal levels
-   write(6,*) ' setting density'
-   rhoNew(1,:,:) = 1000.0
-!  if(nVertLevelsMOD .eq. 3) then
-!      rhoNew(1,2,:) = 1011.0
-!      rhoNew(1,3,:) = 1012.0
-!  endif
-
-   ! basin-mod
-   ! set temperature for isopycnal levels
-   write(6,*) ' setting temperature'
-   vertTempChange = 2.5
-   surfMaxTemp = 13.1
-   surfMinTemp = 10.1
-   do k = 1, nVertLevelsMOD
-        temperatureNew(1,k,:) = (surfMaxTemp - surfMinTemp) * ((-hZLevel(k)+h_total_max)/h_total_max)+ surfMinTemp
-   enddo
-
-   tempHolder = temperatureNew
-
-   y_0 = 200.0e3
-   x_0 = 0.0e3
-   x_1 = 160.0e3
-   x_2 = 110.0e3
-   x_3 = 130.0e3
-   width = 40.0e3
-   do i = 1, nCellsNew
-     cff1 = width * sin (6.0 * 3.141592 * (xCellNew(i) - x_0)/(x_1 - x_0))
-
-     if( yCellNew(i) &lt; y_0 - cff1 ) then
-         do k = 1, nVertLevelsMOD
-            temperatureNew(1,k,i) = temperatureNew(1,k,i) - 1.2
-         end do
-     else if( yCellNew(i) .ge. y_0 - cff1 .and. yCellNew(i) .le. y_0 - cff1+width) then
-         do k = 1, nVertLevelsMOD
-            temperatureNew(1,k,i) = tempHolder(1,k,i) - 1.2*(1.0 -( yCellNew(i) - (y_0 - cff1)) / (1.0 * width))
-         end do
-     endif
-   enddo
-
-   do i = 1, nCellsNew
-     cff1 = 0.5 * width * sin(1.0 * 3.141592 * (xCellNew(i) - x_2)/(x_3 - x_2))
-
-     if( yCellNew(i) .ge. y_0 - cff1-0.5*width .and. yCellNew(i) .le. y_0 - cff1+0.5*width .and. xCellNew(i) .ge. x_2 .and. xCellNew(i) .le. x_3) then
-       do k = 1, nVertLevelsMOD
-         temperatureNew(1,k,i) = temperatureNew(1,k,i) + 0.3 * (1.0 - ( (yCellNew(i)-(y_0-cff1))/(0.5*width)))
-       end do
-     endif
-   end do
-!  do i = 1,nCellsNew
-!     yTrans = 250000.0 + 25000.0 * sin(2.0 * xCellNew(i)/15000.0)
-
-!     if(yCellNew(i) &gt; yTrans + 25000.0) then
-!       maxTemp = 13.0
-!     else if (yCellNew(i) &lt; yTrans - 25000.0) then
-!       maxTemp = 11.8
-!     else
-
-!       maxTemp = surfMinTemp + (surfMaxTemp - surfMinTemp) * (yCellNew(i) - (yTrans - 25000.0))/50000.0
-!       print *,'maxTemp', maxTemp, (yCellNew(i) - (yTrans - 25000.0))/50000.0
-!     endif
-
-
-!     do k = 1,nVertLevelsMOD
-!        temperatureNew(1,k,i) = maxTemp - ((k-1)*vertTempChange/nVertLevelsMOD)
-!     end do
-!  enddo
-
-   ! basin-mod
-   ! set salinity for levels
-   salinityNew(1,:,:) = 35.0
-
-   ! Updating density with linear EOS
-   do i = 1,nCellsNew
-     rhoNew(1,:,i) = 1000.0*(1.0 - 2.5e-4*temperatureNew(1,1,i) + 7.6e-4*salinityNew(1,1,i))
-   enddo
-
-   ! basin-mod
-   ! set forcing for isopycnal levels
-   write(6,*) 'setting u_src - wind forcing'
-   u_srcNew = 0.0
-   write(6,*) ' u_srcNew ', minval(u_srcNew), maxval(u_srcNew)
-
-   ! basin-mod
-   ! set coriolis parameter for grid
-   write(6,*) ' setting Coriolis parameter'
-   ymid = (maxval(yVertexNew(:)) - minval(yVertexNew(:)))/2.0
-   do i = 1,nVerticesNew
-     fVertexNew(i) = f0 + (yVertexNew(i) - ymid) * beta
-   enddo
-
-   ymid = (maxval(yEdgeNew(:)) - minval(yEdgeNew(:)))/2.0
-   do i = 1,nEdgesNew
-     fEdgeNew(i) = f0 + (yEdgeNew(i) - ymid) * beta
-   enddo
-
-
-   write(6,*) ' done not real bathymetry'
-endif   ! if(.not.real_bathymetry) then
-
-
-if(real_bathymetry) then
-
-u_srcNew = 0.0
-do iEdge=1,nEdgesNew
-  xin = xEdgeNew(iEdge)
-  yin = yEdgeNew(iEdge)
-  zin = zEdgeNew(iEdge)
-  rlon = lonEdgeNew(iEdge)/dtr
-  rlat = latEdgeNew(iEdge)/dtr
-  ix = nint(rlon/0.1 - 0.05) + nlon + 1
-  ix = mod(ix,nlon)+1
-  iy = nlat
-  do jcount=1,nlat
-   if(t_lat(jcount).gt.rlat) then
-    iy = jcount
-    exit
-   endif
-  enddo
- !stress = -0.1*cos(3.0*latEdgeNew(iEdge))
- !ulon = stress
- !ulat = 0.0
-  ulon = TAUX(ix,iy)
-  ulat = TAUY(ix,iy)
-  write(6,*) rlon, t_lon(ix), rlat, t_lat(iy)
-  call transform_from_lonlat_to_xyz(xin,yin,zin,ulon,ulat,ux,uy,uz)
-  if(boundaryEdgeNew(1,iEdge).eq.1) then
-    u_srcNew(1,iEdge) = 0.0
-  else
-    iCell1 = cellsOnEdgeNew(1,iEdge)
-    iCell2 = cellsOnEdgeNew(2,iEdge)
-    p(1) = xCellNew(iCell1); p(2) = yCellNew(iCell1); p(3) = zCellNew(iCell1)
-    q(1) = xCellNew(iCell2); q(2) = yCellNew(iCell2); q(3) = zCellNew(iCell2)
-    q = q - p
-    call unit_vector_in_3space(q)
-    u_srcNew(1,iEdge) = ux*q(1) + uy*q(2) + uz*q(3)
-  endif
-enddo
-

-!set tracers at a first guess
-temperatureNew = -99.0
-salinityNew = -99.0
-do iCell=1,nCellsNew
-do k = 1,maxLevelCellNew(iCell)
-  temperatureNew(1,k,iCell) = 20.0 - 10.0*k/nVertLevelsMod
-  salinityNew(1,k,iCell) = 34.0  ! salinity
-enddo
-enddo
-
-! update T and S field with WOCE data
-if(l_woce) then
-iNoData = 0
-do iCell=1,nCellsNew
-  hNew(1,:,iCell) = dz(:)
-  hZLevel = dz
-  if(mod(iCell,100).eq.0) write(6,*) 'l_woce t and s',iCell
-  rlon = lonCellNew(iCell)/dtr
-  rlat = latCellNew(iCell)/dtr
-  ix = nint(rlon/0.1 - 0.05) + nlon + 1
-  ix = mod(ix,nlon)+1
-  iy = nlat
-  do j=1,nlat
-   if(t_lat(j).gt.rlat) then
-    iy = j
-    exit
-   endif
-  enddo
-  do k=1,maxLevelCellNew(iCell)
-    ndata = 0; temp_t = 0; temp_s = 0; kdata(:) = 0
-    do i=-15,15
-      ixt = ix + 8*i
-      if(ixt.lt.1) then
-        ixt = ixt + nlon
-      elseif(ixt.gt.nlon) then
-        ixt = ixt - nlon
-      endif
-      do j=-15,15
-        iyt = iy + 8*j
-        flag_lat = .true.
-        if(iyt.lt.1.or.iyt.gt.nlat) then
-          iyt = 1
-          flag_lat = .false.
-        endif
-        if(TEMP(ixt,iyt,k).gt.-10.0.and.flag_lat) then
-          ndata = ndata + 1
-          temp_t = temp_t + TEMP(ixt,iyt,k)
-          temp_s = temp_s + SALT(ixt,iyt,k)
-        endif
-      enddo
-    enddo
-
-    if(ndata.gt.0) then
-      temperatureNew(1,k,iCell) = temp_t / float(ndata)
-      salinityNEW(1,k,iCell) = temp_s / float(ndata)
-      kdata(k) = 1
-    else
-      if(k.eq.1) iNoData = iNoData + 1
-      if(k.ge.3) then
-        if(kdata(k-1).eq.1) maxLevelCellNew(iCell) = k-1
-      endif
-    endif
-
-  enddo
-
-enddo
-
-! do a couple of smoothing passes
-do iter=1,5
-do iCell=1,nCellsNew
-do k=1,maxLevelCellNew(iCell)
-  ndata=1
-  temp_t = temperatureNew(1,k,iCell)
-  temp_s = salinityNew(1,k,iCell)
-  do j=1,nEdgesOnCellNew(iCell)
-    jCell = cellsOnCellNew(j,iCell)
-    if(jCell.gt.0) then
-    if(maxLevelCellNew(jCell).ge.k) then
-      temp_t = temp_t + temperatureNew(1,k,jCell)
-      temp_s = temp_s + salinityNew(1,k,jCell)
-      ndata = ndata + 1
-    endif
-    endif
-  enddo
-  temperatureNew(1,k,iCell) = temp_t / ndata
-  salinityNew(1,k,iCell) = temp_s / ndata
-enddo
-enddo
-write(6,*) maxval(temperatureNew(1,1,:)),maxval(salinityNew(1,1,:))
-enddo
-
-write(6,*) iNoData, nCellsNew
-
-temperatureRestoreNew(:) = temperatureNew(1,1,:)
-salinityRestoreNew(:) = salinityNew(1,1,:)
-
-endif
-
-endif
-
-write(6,*) ' done get_init_conditions'
-
-end subroutine get_init_conditions
-
-
-subroutine error_checking
-real :: p(3), q(3), r(3), angle, s(3), t(3), dot, mindot, maxdot, b(vertexDegree)
-real :: work(nCellsNew)
-
-
-! write
-write(6,*)
-write(6,*) ' error checking '
-write(6,*)
-
-! check to see if every edge is normal to associated cells
-mindot =  2
-maxdot = -2
-do iEdge=1,nEdgesNew
-  if(boundaryEdgeNew(1,iEdge).eq.1) cycle
-  iCell1 = cellsOnEdgeNew(1,iEdge)
-  iCell2 = cellsOnEdgeNew(2,iEdge)
-  p(1)=xCellNew(iCell1); p(2)=yCellNew(iCell1); p(3)=zCellNew(iCell1)
-  q(1)=xCellNew(iCell2); q(2)=yCellNew(iCell2); q(3)=zCellNew(iCell2)
-  r(1)=xEdgeNew(iEdge);  r(2)=yEdgeNew(iEdge);  r(3)=zEdgeNew(iEdge)
-  call unit_vector_in_3space(p)
-  call unit_vector_in_3space(q)
-  call unit_vector_in_3space(r)
-  t = q - p
-  s = r - p
-  call unit_vector_in_3space(t)
-  call unit_vector_in_3space(s)
-  dot = s(1)*t(1)+s(2)*t(2)+s(3)*t(3)
-  if(dot.lt.mindot) mindot=dot
-  if(dot.gt.maxdot) maxdot=dot
-enddo
-write(6,10) 'alignment of edges and cells (should be ones)', mindot, maxdot
-10 format(a60,5x,2e15.5)
-
-! check to see if every segments connecting cells and vertices are orothogonal'
-mindot =  2
-maxdot = -2
-do iEdge=1,nEdgesNew
-  if(boundaryEdgeNew(1,iEdge).eq.1) cycle
-  iCell1 = cellsOnEdgeNew(1,iEdge)
-  iCell2 = cellsOnEdgeNew(2,iEdge)
-  iVertex1 = verticesOnEdgeNew(1,iEdge)
-  iVertex2 = verticesOnEdgeNew(2,iEdge)
-  p(1)=xCellNew(iCell1); p(2)=yCellNew(iCell1); p(3)=zCellNew(iCell1)
-  q(1)=xCellNew(iCell2); q(2)=yCellNew(iCell2); q(3)=zCellNew(iCell2)
-  r(1)=xVertexNew(iVertex1); r(2)=yVertexNew(iVertex1); r(3)=zVertexNew(iVertex1)
-  s(1)=xVertexNew(iVertex2); s(2)=yVertexNew(iVertex2); s(3)=zVertexNew(iVertex2)
-  call unit_vector_in_3space(p)
-  call unit_vector_in_3space(q)
-  call unit_vector_in_3space(r)
-  call unit_vector_in_3space(s)
-  t = q - p
-  s = s - r
-  call unit_vector_in_3space(t)
-  call unit_vector_in_3space(s)
-  dot = s(1)*t(1)+s(2)*t(2)+s(3)*t(3)
-  if(dot.lt.mindot) mindot=dot
-  if(dot.gt.maxdot) maxdot=dot
-enddo
-write(6,10) 'orthogonality of cell and vertex edges (should be zeros)', mindot, maxdot
-
-! check that the kiteareas sum to the areatriangle
-mindot =  2
-maxdot = -2
-do iVertex=1,nVerticesNew
-  b = 0
-  do i=1,vertexDegree
-    b(i) = kiteAreasOnVertexNew(i,iVertex)
-  enddo
-  angle = sum(b)
-  if(angle - areaTriangleNew(iVertex).lt.mindot) mindot = angle - areaTriangleNew(iVertex)
-  if(angle - areaTriangleNew(iVertex).gt.maxdot) maxdot = angle - areaTriangleNew(iVertex)
-enddo
-write(6,10) ' error in sum of kites and triangles (should be zeroes)', mindot, maxdot
-
-! check that the kiteareas sum to the areaCell
-mindot =  2
-maxdot = -2
-work = 0
-do iVertex=1,nVerticesNew
-  iCell1 = cellsOnVertexNew(1,iVertex)
-  iCell2 = cellsOnVertexNew(2,iVertex)
-  iCell3 = cellsOnVertexNew(3,iVertex)
-  if(iCell1.ne.0) work(iCell1) = work(iCell1) + kiteAreasOnVertexNew(1,iVertex)
-  if(iCell2.ne.0) work(iCell2) = work(iCell2) + kiteAreasOnVertexNew(2,iVertex)
-  if(iCell3.ne.0) work(iCell3) = work(iCell3) + kiteAreasOnVertexNew(3,iVertex)
-enddo
-mindot = minval(areaCellNew - work)
-maxdot = maxval(areaCellNew - work)
-write(6,10) ' error in sum of kites and cells (should be zeroes)', mindot, maxdot
-
-!check for connectivity inverses for cells/edges
-do iCell=1,nCellsNew
-  do i=1,nEdgesOnCellNew(iCell)
-    iEdge=edgesOnCellNew(i,iCell)
-    if(iEdge.le.0) stop ' iEdge le 0'
-    iCell1 = cellsOnEdgeNew(1,iEdge)
-    iCell2 = cellsOnEdgeNew(2,iEdge)
-    if(iCell1.ne.iCell.and.iCell2.ne.iCell) stop ' cells/edges inverse failed'
-  enddo
-enddo
-write(6,*) ' cellsOnEdge and edgesOnCell are duals for every cell/edge combination'
-
-!check for connectivity inverses for cells/vertices
-do iCell=1,nCellsNew
-  do i=1,nEdgesOnCellNew(iCell)
-    iVertex = verticesOnCellNew(i,iCell)
-    if(iVertex.le.0) stop ' iVertex le 0'
-    iCell1 = cellsOnVertexNew(1,iVertex)
-    iCell2 = cellsOnVertexNew(2,iVertex)
-    iCell3 = cellsOnVertexNew(3,iVertex)
-    if(iCell1.ne.iCell.and.iCell2.ne.iCell.and.iCell3.ne.iCell) stop ' cells/vertices inverse failed'
-  enddo
-enddo
-write(6,*) ' cellsOnVertex and verticesOnCell are duals for every cell/vertex combination'
-
-!check edgesOnEdge
-do iEdge=1,nEdgesNew
-  iCell1 = cellsOnEdgeNew(1,iEdge)
-  iCell2 = cellsOnEdgeNew(2,iEdge)
-  if(nEdgesOnEdgeNew(iEdge).eq.0) then
-    if(boundaryEdgeNew(1,iEdge).ne.1) stop ' stopping boundaryEdgeNew'
-  endif
-  do i=1,nEdgesOnEdgeNew(iEdge)
-    jEdge = edgesOnEdgeNew(i,iEdge)
-    jCell1 = cellsOnEdgeNew(1,jEdge)
-    jCell2 = cellsOnEdgeNew(2,jEdge)
-    if(jCell1.ne.iCell1.and.jCell1.ne.iCell2) then
-    if(jCell2.ne.iCell1.and.jCell2.ne.iCell2) then
-          write(6,*) 'error in edgesOnEdge'
-          write(6,*) iCell1, iCell2, jCell1, jCell2
-          stop
-    endif
-    endif
-  enddo
-enddo
-write(6,*) ' edgesOnEdge is consistent with cellsOnEdge'
-
-end subroutine error_checking
-
-
-subroutine copy_dimensions
-
-maxEdgesNew = maxEdges
-maxEdges2New = maxEdges2
-TWONew = TWO
-vertexDegreeNew = vertexDegree
-nVertLevelsNew = nVertLevelsMod
-
-write(6,*)
-write(6,*) ' new dimensions '
-write(6,*) ' maxEdgesNew     : ', maxEdgesNew
-write(6,*) ' maxEdges2New    : ', maxEdges2New
-write(6,*) ' TWONew          : ', TWONew
-write(6,*) ' vertexDegreeNew : ', vertexDegreeNew
-write(6,*) ' nVertLevelsNew  : ', nVertLevelsNew
-
-end subroutine copy_dimensions
-
-
-
-subroutine read_grid
-implicit none
-
-call read_netcdf_init(nCells, nEdges, nVertices, maxEdges,maxEdges2,&amp;
-                       nVertLevels,TWO,vertexDegree)
-
-write(6,*) ' init from grid '
-write(6,*) 'nCells        :', nCells
-write(6,*) 'nEdges        :', nEdges
-write(6,*) 'nVertices     :', nVertices
-write(6,*) 'maxEdges      :', maxEdges
-write(6,*) 'maxEdges2     :', maxEdges2
-write(6,*) 'nVertLevels   :', nVertLevels
-write(6,*) 'vertexDegree  :', vertexDegree
-write(6,*) 'TWO           :', TWO
-
-allocate(xCell(nCells))
-allocate(yCell(nCells))
-allocate(zCell(nCells))
-allocate(latCell(nCells))
-allocate(lonCell(nCells))
-allocate(meshDensity(nCells))
-allocate(xEdge(nEdges))
-allocate(yEdge(nEdges))
-allocate(zEdge(nEdges))
-allocate(latEdge(nEdges))
-allocate(lonEdge(nEdges))
-allocate(xVertex(nVertices))
-allocate(yVertex(nVertices))
-allocate(zVertex(nVertices))
-allocate(latVertex(nVertices))
-allocate(lonVertex(nVertices))
-allocate(dcEdge(nEdges))
-allocate(dvEdge(nEdges))
-
-allocate(indexToCellID(nCells))
-allocate(indexToEdgeID(nEdges))
-allocate(indexToVertexID(nVertices))
-
-allocate(cellsOnEdge(TWO,nEdges))
-allocate(nEdgesOnCell(nCells))
-allocate(nEdgesOnEdge(nEdges))
-allocate(edgesOnCell(maxEdges,nCells))
-allocate(edgesOnEdge(maxEdges2,nEdges))
-allocate(weightsOnEdge(maxEdges2,nEdges))
-
-allocate(angleEdge(nEdges))
-allocate(areaCell(nCells))
-allocate(areaTriangle(nVertices))
-allocate(cellsOnCell(maxEdges,nCells))
-allocate(verticesOnCell(maxEdges,nCells))
-allocate(verticesOnEdge(TWO,nEdges))
-allocate(edgesOnVertex(vertexDegree,nVertices))
-allocate(cellsOnVertex(vertexDegree,nVertices))
-allocate(kiteAreasOnVertex(vertexDegree,nVertices))
-
-allocate(fEdge(nEdges))
-allocate(fVertex(nVertices))
-allocate(h_s(nCells))
-allocate(work1(nCells))
-allocate(u_src(nVertLevels,nEdges))
-allocate(u(1,nVertLevels,nEdges))
-allocate(v(1,nVertLevels,nEdges))
-allocate(h(1,nVertLevels,nCells))
-allocate(rho(1,nVertLevels,nCells))
-
-xCell=0; yCell=0; zCell=0; latCell=0; lonCell=0; meshDensity=1.0
-xEdge=0; yEdge=0; zEdge=0; latEdge=0; lonEdge=0
-xVertex=0; yVertex=0; zVertex=0; latVertex=0; lonVertex=0
-
-indexToCellID=0; indexToEdgeID=0; indexToVertexID=0
-cellsOnEdge=0; nEdgesOnCell=0; edgesOnCell=0
-edgesOnEdge=0; weightsOnEdge=0
-angleEdge=0; areaCell=0; areaTriangle=0
-cellsOnCell=0; verticesOnCell=0; verticesOnEdge=0
-edgesOnVertex=0; cellsOnVertex=0; kiteAreasOnVertex=0
-
-fEdge=0; fVertex=0; h_s=0; u_src=0; work1=0
-u=0; v=0; h=0; rho=0
-
-
-call  read_netcdf_fields( &amp;
-                    time, &amp;
-                    latCell, &amp;
-                    lonCell, &amp;
-                    meshDensity, &amp;
-                    xCell, &amp;
-                    yCell, &amp;
-                    zCell, &amp;
-                    indexToCellID, &amp;
-                    latEdge, &amp;
-                    lonEdge, &amp;
-                    xEdge, &amp;
-                    yEdge, &amp;
-                    zEdge, &amp;
-                    indexToEdgeID, &amp;
-                    latVertex, &amp;
-                    lonVertex, &amp;
-                    xVertex, &amp;
-                    yVertex, &amp;
-                    zVertex, &amp;
-                    indexToVertexID, &amp;
-                    cellsOnEdge, &amp;
-                    nEdgesOnCell, &amp;
-                    nEdgesOnEdge, &amp;
-                    edgesOnCell, &amp;
-                    edgesOnEdge, &amp;
-                    weightsOnEdge, &amp;
-                    dvEdge, &amp;
-                    dcEdge, &amp;
-                    angleEdge, &amp;
-                    areaCell, &amp;
-                    areaTriangle, &amp;
-                    cellsOnCell, &amp;
-                    verticesOnCell, &amp;
-                    verticesOnEdge, &amp;
-                    edgesOnVertex, &amp;
-                    cellsOnVertex, &amp;
-                    kiteAreasOnVertex, &amp;
-                    fEdge, &amp;
-                    fVertex, &amp;
-                    h_s, &amp;
-                    u, &amp;
-                    v, &amp;
-                    h &amp;
-                   )
-
-write(6,*) ' values from read grid, min/max'
-write(6,*) ' latCell : ', minval(latCell), maxval(latCell)
-write(6,*) ' lonCell : ', minval(lonCell), maxval(lonCell)
-write(6,*) ' meshDensity : ', minval(meshDensity),maxval(meshDensity)
-write(6,*) ' xCell : ', minval(xCell), maxval(xCell)
-write(6,*) ' yCell : ', minval(yCell), maxval(yCell)
-write(6,*) ' zCell : ', minval(zCell), maxval(zCell)
-write(6,*) ' indexToCellID : ', minval(indexToCellID), maxval(indexToCellID)
-write(6,*) ' latEdge : ', minval(latEdge), maxval(latEdge)
-write(6,*) ' lonEdge : ', minval(lonEdge), maxval(lonEdge)
-write(6,*) ' xEdge : ', minval(xEdge), maxval(xEdge)
-write(6,*) ' yEdge : ', minval(yEdge), maxval(yEdge)
-write(6,*) ' zEdge : ', minval(zEdge), maxval(zEdge)
-write(6,*) ' indexToEdgeID : ', minval(indexToEdgeID), maxval(indexToEdgeID)
-write(6,*) ' latVertex : ', minval(latVertex), maxval(latVertex)
-write(6,*) ' lonVertex : ', minval(lonVertex), maxval(lonVertex)
-write(6,*) ' xVertex : ', minval(xVertex), maxval(xVertex)
-write(6,*) ' yVertex : ', minval(yVertex), maxval(yVertex)
-write(6,*) ' zVertex : ', minval(zVertex), maxval(zVertex)
-write(6,*) ' indexToVertexID : ', minval(indexToVertexID), maxval(indexToVertexID)
-write(6,*) ' cellsOnEdge : ', minval(cellsOnEdge), maxval(cellsOnEdge)
-write(6,*) ' nEdgesOnCell : ', minval(nEdgesOnCell), maxval(nEdgesOnCell)
-write(6,*) ' nEdgesOnEdge : ', minval(nEdgesOnEdge), maxval(nEdgesOnEdge)
-write(6,*) ' edgesOnCell : ', minval(edgesOnCell), maxval(edgesOnCell)
-write(6,*) ' edgesOnEdge : ', minval(edgesOnEdge), maxval(edgesOnEdge)
-write(6,*) ' weightsOnEdge : ', minval(weightsOnEdge), maxval(weightsOnEdge)
-write(6,*) ' dvEdge : ', minval(dvEdge), maxval(dvEdge)
-write(6,*) ' dcEdge : ', minval(dcEdge), maxval(dcEdge)
-write(6,*) ' angleEdge : ', minval(angleEdge), maxval(angleEdge)
-write(6,*) ' areaCell : ', minval(areaCell), maxval(areaCell)
-write(6,*) ' areaTriangle : ', minval(areaTriangle), maxval(areaTriangle)
-write(6,*) ' cellsOnCell : ', minval(cellsOnCell), maxval(cellsOnCell)
-write(6,*) ' verticesOnCell : ', minval(verticesOnCell), maxval(verticesOnCell)
-write(6,*) ' verticesOnEdge : ', minval(verticesOnEdge), maxval(verticesOnEdge)
-write(6,*) ' edgesOnVertex : ', minval(edgesOnVertex), maxval(edgesOnVertex)
-write(6,*) ' cellsOnVertex : ', minval(cellsOnVertex), maxval(cellsOnVertex)
-write(6,*) ' kiteAreasOnVertex : ', minval(kiteAreasOnVertex), maxval(kiteAreasOnVertex)
-write(6,*) ' fEdge : ', minval(fEdge), maxval(fEdge)
-write(6,*) ' fVertex : ', minval(fVertex), maxval(fVertex)
-write(6,*) ' h_s : ', minval(h_s), maxval(h_s)
-write(6,*) ' u : ', minval(u), maxval(u)
-write(6,*) ' v : ', minval(v), maxval(v)
-write(6,*) ' h : ', minval(h), maxval(h)
-
-end subroutine read_grid
-
-
-subroutine write_grid
-implicit none
-
-if(on_a_sphere.eq.'YES              ') then
-   xCellNew = xCellNew * sphere_radius
-   yCellNew = yCellNew * sphere_radius
-   zCellNew = zCellNew * sphere_radius
-   xEdgeNew = xEdgeNew * sphere_radius
-   yEdgeNew = yEdgeNew * sphere_radius
-   zEdgeNew = zEdgeNew * sphere_radius
-   xVertexNew = xVertexNew * sphere_radius
-   yVertexNew = yVertexNew * sphere_radius
-   zVertexNew = zVertexNew * sphere_radius
-   dcEdgeNew = dcEdgeNew * sphere_radius
-   dvEdgeNew = dvEdgeNew * sphere_radius
-   areaCellNew = areaCellNew * (sphere_radius)**2
-   areaTriangleNew = areaTriangleNew * (sphere_radius)**2
-   kiteAreasOnVertexNew = kiteAreasOnVertexNew * (sphere_radius)**2
-endif
-
-call write_netcdf_init( &amp;
-                nCellsNew, &amp;
-                nEdgesNew, &amp;
-                nVerticesNew, &amp;
-                maxEdgesNew, &amp;
-                nVertLevelsNew, &amp;
-                vertexDegreeNew, &amp;
-                sphere_radius, &amp;
-                on_a_sphere &amp;
-                )
-
-call write_netcdf_fields( &amp;
-                    1, &amp;
-                    latCellNew, &amp;
-                    lonCellNew, &amp;
-                    meshDensityNew, &amp;
-                    xCellNew, &amp;
-                    yCellNew, &amp;
-                    zCellNew, &amp;
-                    indexToCellIDNew, &amp;
-                    latEdgeNew, &amp;
-                    lonEdgeNew, &amp;
-                    xEdgeNew, &amp;
-                    yEdgeNew, &amp;
-                    zEdgeNew, &amp;
-                    indexToEdgeIDNew, &amp;
-                    latVertexNew, &amp;
-                    lonVertexNew, &amp;
-                    xVertexNew, &amp;
-                    yVertexNew, &amp;
-                    zVertexNew, &amp;
-                    indexToVertexIDNew, &amp;
-                    maxLevelCellNew, &amp;
-                    cellsOnEdgeNew, &amp;
-                    nEdgesOnCellNew, &amp;
-                    nEdgesOnEdgeNew, &amp;
-                    edgesOnCellNew, &amp;
-                    edgesOnEdgeNew, &amp;
-                    weightsOnEdgeNew, &amp;
-                    dvEdgeNew, &amp;
-                    dcEdgeNew, &amp;
-                    angleEdgeNew, &amp;
-                    areaCellNew, &amp;
-                    areaTriangleNew, &amp;
-                    cellsOnCellNew, &amp;
-                    verticesOnCellNew, &amp;
-                    verticesOnEdgeNew, &amp;
-                    edgesOnVertexNew, &amp;
-                    cellsOnVertexNew, &amp;
-                    kiteAreasOnVertexNew, &amp;
-                    fEdgeNew, &amp;
-                    fVertexNew, &amp;
-                    h_sNew, &amp;
-                    boundaryEdgeNew, &amp;
-                    boundaryVertexNew, &amp;
-                    u_srcNew, &amp;
-                    uNew, &amp;
-                    vNew, &amp;
-                    hNew, &amp;
-                    rhoNew, &amp;
-                    temperatureNew, &amp;
-                    salinityNew, &amp;
-                    tracer1New, &amp;
-                    temperatureRestoreNew, &amp;
-                    salinityRestoreNew, &amp;
-                    hZLevel &amp;
-                   )
-
-call write_netcdf_finalize
-
-if(on_a_sphere.eq.'YES              ') then
-   xCellNew = xCellNew / sphere_radius
-   yCellNew = yCellNew / sphere_radius
-   zCellNew = zCellNew / sphere_radius
-   xEdgeNew = xEdgeNew / sphere_radius
-   yEdgeNew = yEdgeNew / sphere_radius
-   zEdgeNew = zEdgeNew / sphere_radius
-   xVertexNew = xVertexNew / sphere_radius
-   yVertexNew = yVertexNew / sphere_radius
-   zVertexNew = zVertexNew / sphere_radius
-   dcEdgeNew = dcEdgeNew / sphere_radius
-   dvEdgeNew = dvEdgeNew / sphere_radius
-   areaCellNew = areaCellNew / (sphere_radius)**2
-   areaTriangleNew = areaTriangleNew / (sphere_radius)**2
-   kiteAreasOnVertexNew = kiteAreasOnVertexNew / (sphere_radius)**2
-endif
-
-end subroutine write_grid
-
-! Step 5: Check the depth routine define_kmt
-subroutine define_kmt
-implicit none
-real (kind=4), allocatable, dimension(:) :: x,y, work_kmt
-real (kind=4), allocatable, dimension(:,:) :: ztopo
-integer :: nx, ny, inx, iny, ix, iy, kmt_neighbor_max
-real :: pi, dtr, zdata, rlon, rlat, r, ymin, ymax, xmin, xmax
-real :: latmin, latmax, lonmin, lonmax
-logical :: flag, kmt_flag
-pi = 4.0*atan(1.0)
-dtr = pi / 180.0
-
-allocate(kmt(nCells))
-kmt = 0
-
-if(.not.real_bathymetry) then
-    kmt = nVertLevelsMOD
-    if(on_a_sphere.eq.'YES              ') then
-        write(6,*) 'Working on a sphere'
-        latmin = -30*dtr
-        latmax = +30*dtr
-        lonmin = +10*dtr
-        lonmax = +70*dtr
-        write(6,*) ' lat min ', latmin
-        write(6,*) ' lat max ', latmax
-        where(latCell.lt.latmin) kmt = 0
-        where(latCell.gt.latmax) kmt = 0
-        where(lonCell.lt.lonmin) kmt = 0
-        where(lonCell.gt.lonmax) kmt = 0
-    else
-        ! solid boundary in y
-        ymin = minval(yCell)
-        write(6,*) ' minimum yCell ', ymin
-        ymax = maxval(yCell)
-        write(6,*) ' maximum yCell ', ymax
-        where(yCell.lt.1.001*ymin) kmt = 0
-        where(yCell.gt.0.999*ymax) kmt = 0
-
-!       xmin = minval(xCell)
-!       xmax = maxval(xCell)
-!       where(xCell.lt.1.001*xmin) kmt = 0
-!       where(xCell.gt.0.999*xmax) kmt = 0
-
-     !  ! solid boundary in x
-     !  xmin = minval(xCell)
-     !  write(6,*) ' minimum xCell ', xmin
-     !  xmax = maxval(xCell)
-     !  write(6,*) ' maximum xCell ', xmax
-     !  where(xCell.lt.xmin+dc/1.5) kmt = 0
-     !  where(xCell.gt.xmax-dc/1.5) kmt = 0
-    endif
-
-    
-    allocate(work_kmt(nCells))
-    work_kmt = 0.0
-    where(kmt.eq.0) work_kmt=1.0
-    write(6,*) 'number of cells culled ',sum(work_kmt)
-    deallocate(work_kmt)
-endif
-
-if(real_bathymetry) then
-    nx = 10800
-    ny = 5400
-    allocate(x(nx))
-    allocate(y(ny))
-    allocate(ztopo(nx,ny))
-    x = 0.0
-    y = 0.0
-    ztopo = 0.0
-    write(6,*) ' ztopo ', minval(ztopo), maxval(ztopo)
-    call read_topo_init( inx, iny)
-    if(inx.ne.nx) stop ' nx topo'
-    if(iny.ne.ny) stop ' ny topo'
-    call read_topo_fields(x,y,ztopo)
-    call read_topo_finalize()
-    write(6,*) minval(x), maxval(x), x(1)
-    write(6,*) minval(y), maxval(y), y(1)
-    write(6,*) minval(ztopo), maxval(ztopo)
-
-    do iCell=1,nCells
-        rlon = lonCell(iCell) / dtr
-        rlat = latCell(iCell) / dtr
-        ix = nint((rlon+180)*30) + nx
-        ix = mod(ix,nx)+1
-        iy = nint((rlat+90 )*30)
-        ix = max(1,ix); ix = min(nx,ix)
-        iy = max(1,iy); iy = min(ny,iy)
-
-        zdata = ztopo(ix,iy)
-
-        if(zdata.lt.0.0) then
-            zdata = -zdata
-            r = 0
-            kmt_flag=.false.
-            do k=1,nVertLevelsMod
-                if(.not.kmt_flag) then
-                    r = r + dz(k)
-                    if(r.gt.zdata) then
-                        kmt(iCell) = k
-                        kmt_flag = .true.
-                    endif
-                endif
-            enddo
-            if(kmt(iCell).eq.0) kmt(iCell)=nVertLevelsMod
-            ! write(6,*) kmt(iCell)
-        endif
-
-        ! if(zdata.lt.0.0) kmt(iCell) = nVertLevelsMod
-
-    enddo
-
-    deallocate(x)
-    deallocate(y)
-    deallocate(ztopo)
-endif
-
-! Eliminate isolated ocean cells, and make these isolated deep cells
-! flush with the deepest neighbor.
-do iCell=1,nCells
-   kmt_neighbor_max = 0
-   do j=1,nEdgesOnCell(iCell)
-      iCell1 = cellsOnCell(j,iCell)
-      kmt_neighbor_max = max(kmt_neighbor_max,kmt(iCell1))
-   enddo
-   kmt(iCell) = min(kmt(iCell),kmt_neighbor_max)
-enddo
-
-if(eliminate_inland_seas) then
-call eliminateLoops(nCells,nEdges,nVertices,maxEdges,vertexDegree, &amp;
-                    nEdgesOnCell, cellsOnCell, verticesOnEdge, cellsOnVertex, edgesOnCell, lonCell, latCell, &amp;
-                    xCell, yCell, zCell, xEdge, yEdge, zEdge, xVertex, yVertex, zVertex, &amp;
-                    KMT)
-endif
-
-if(real_bathymetry) then
-    where(kmt.eq.1) kmt=3
-    where(kmt.eq.2) kmt=3
-endif
-
-end subroutine define_kmt
-
-
-
-subroutine define_mapping
-implicit none
-
-allocate(cellMap(nCells))
-allocate(edgeMap(nEdges))
-allocate(vertexMap(nVertices))
-cellMap = 0; edgeMap = 0; vertexMap = 0
-
-j=1
-do i=1,nCells
-if(kmt(i).ne.0) then
-    cellMap(i) = j
-    j=j+1
-endif
-write(10,*) i, cellMap(i)
-enddo
-
-j=1
-do i=1,nEdges
-iCell1 = cellsOnEdge(1,i)
-iCell2 = cellsOnEdge(2,i)
-if(kmt(iCell1).ne.0.or.kmt(iCell2).ne.0) then
-    edgeMap(i)=j
-    j=j+1
-endif
-write(11,*) i,edgeMap(i)
-enddo
-
-j=1
-do i=1,nVertices
-iCell1 = cellsOnVertex(1,i)
-iCell2 = cellsOnVertex(2,i)
-iCell3 = cellsOnVertex(3,i)
-if(kmt(iCell1).ne.0.or.kmt(iCell2).ne.0.or.kmt(iCell3).ne.0) then
-    vertexMap(i)=j
-    j=j+1
-endif
-write(12,*) i,vertexMap(i)
-enddo
-
-nCellsNew = 0
-do i=1,nCells
-if(cellMap(i).ne.0) nCellsNew = nCellsNew + 1
-enddo
-
-nEdgesNew = 0
-do i=1,nEdges
-if(edgeMap(i).ne.0) nEdgesNew = nEdgesNew + 1
-enddo
-
-nVerticesNew = 0
-do i=1,nVertices
-if(vertexMap(i).ne.0) nVerticesNew = nVerticesNew + 1
-enddo
-
-write(6,*) ' mesh mapping found '
-write(6,*)  nCells, nCellsNew
-write(6,*)  nEdges, nEdgesNew
-write(6,*)  nVertices, nVerticesNew
-
-allocate(indexToCellIDNew(nCellsNew))
-allocate(indexToEdgeIDNew(nEdgesNew))
-allocate(indexToVertexIDNew(nVerticesNew))
-indextoCellIDNew = 0; indexToEdgeIDNew = 0; indexToVertexIDNew = 0
-
-do i=1,nCellsNew
-indexToCellIDNew(i)=i
-enddo
-
-do i=1,nEdgesNew
-indexToEdgeIDNew(i)=i
-enddo
-
-do i=1,nVerticesNew
-indexToVertexIDNew(i)=i
-enddo
-
-end subroutine define_mapping
-
-
-subroutine map_vectors
-implicit none
-
-allocate(xCellNew(nCellsNew))
-allocate(yCellNew(nCellsNew))
-allocate(zCellNew(nCellsNew))
-allocate(normalsNew(3,nEdgesNew))
-allocate(latCellNew(nCellsNew))
-allocate(lonCellNew(nCellsNew))
-allocate(meshDensityNew(nCellsNew))
-allocate(xEdgeNew(nEdgesNew))
-allocate(yEdgeNew(nEdgesNew))
-allocate(zEdgeNew(nEdgesNew))
-allocate(latEdgeNew(nEdgesNew))
-allocate(lonEdgeNew(nEdgesNew))
-allocate(xVertexNew(nVerticesNew))
-allocate(yVertexNew(nVerticesNew))
-allocate(zVertexNew(nVerticesNew))
-allocate(latVertexNew(nVerticesNew))
-allocate(lonVertexNew(nVerticesNew))
-allocate(dcEdgeNew(nEdgesNew))
-allocate(dvEdgeNew(nEdgesNew))
-allocate(angleEdgeNew(nEdgesNew))
-allocate(areaCellNew(nCellsNew))
-allocate(areaTriangleNew(nVerticesNew))
-allocate(maxLevelCellNew(nCellsNew))
-allocate(depthCell(nCellsNew))
-
-allocate(fEdgeNew(nEdgesNew))
-allocate(fVertexNew(nVerticesNew))
-allocate(h_sNew(nCellsNew))
-allocate(u_srcNew(nVertLevelsNew,nEdgesNew))
-allocate(uNew(1,nVertLevelsNew,nEdgesNew))
-allocate(vNew(1,nVertLevelsNew,nEdgesNew))
-allocate(hNew(1,nVertLevelsNew,nCellsNew))
-allocate(hZLevel(nVertLevelsNew))
-allocate(rhoNew(1,nVertLevelsNew,nCellsNew))
-allocate(temperatureNew(1,nVertLevelsNew,nCellsNew))
-allocate(salinityNew(1,nVertLevelsNew,nCellsNew))
-allocate(tracer1New(1,nVertLevelsNew,nCellsNew))
-
-allocate(temperatureRestoreNew(nCellsNew))
-allocate(salinityRestoreNew(nCellsNew))
-
-xCellNew=0; yCellNew=0; zCellNew=0; latCellNew=0; lonCellNew=0; meshDensityNew=1.0
-xEdgeNew=0; yEdgeNew=0; zEdgeNew=0; latEdgeNew=0; lonEdgeNew=0
-xVertexNew=0; yVertexNew=0; zVertexNew=0; latVertexNew=0; lonVertexNew=0
-
-fEdgeNew=0; fVertexNew=0; h_sNew=0; u_srcNew=0
-uNew=0; vNew=0; hNew=0; rhoNew=0
-temperatureNew=0; salinityNew=0; tracer1New=0;
-
-temperatureRestoreNew = 0.0
-salinityRestoreNew = 0.0
-
-
-do i=1,nCells
-jNew = cellMap(i)
-if(jNew.ne.0) then
-    xCellNew(jNew)=xCell(i)
-    yCellNew(jNew)=yCell(i)
-    zCellNew(jNew)=zCell(i)
-    latCellNew(jNew)=latCell(i)
-    lonCellNew(jNew)=lonCell(i)
-    meshDensityNew(jNew)=meshDensity(i)
-    areaCellNew(jNew)=areaCell(i)
-    maxLevelCellNew(jNew) = kmt(i)
-    depthCell(jNew) = kmt(i)
-endif
-enddo
-
-do i=1,nEdges
-jNew = edgeMap(i)
-if(jNew.ne.0) then
-    xEdgeNew(jNew)=xEdge(i)
-    yEdgeNew(jNew)=yEdge(i)
-    zEdgeNew(jNew)=zEdge(i)
-    latEdgeNew(jNew)=latEdge(i)
-    lonEdgeNew(jNew)=lonEdge(i)
-    dcEdgeNew(jNew) = dcEdge(i)
-    dvEdgeNew(jNew) = dvEdge(i)
-    fEdgeNew(jNew) = fEdge(i)
-    angleEdgeNew(jNew) = angleEdge(i)
-endif
-enddo
-
-do i=1,nVertices
-jNew = vertexMap(i)
-if(jNew.ne.0) then
-    xVertexNew(jNew)=xVertex(i)
-    yVertexNew(jNew)=yVertex(i)
-    zVertexNew(jNew)=zVertex(i)
-    latVertexNew(jNew)=latVertex(i)
-    lonVertexNew(jNew)=lonVertex(i)
-    fVertexNew(jNew)=fVertex(i)
-    areaTriangleNew(jNew)=areaTriangle(i)
-endif
-enddo
-
-deallocate(xCell)
-deallocate(yCell)
-deallocate(zCell)
-deallocate(latCell)
-deallocate(lonCell)
-deallocate(meshDensity)
-deallocate(xEdge)
-deallocate(yEdge)
-deallocate(zEdge)
-deallocate(latEdge)
-deallocate(lonEdge)
-deallocate(xVertex)
-deallocate(yVertex)
-deallocate(zVertex)
-deallocate(latVertex)
-deallocate(lonVertex)
-deallocate(dcEdge)
-deallocate(dvEdge)
-
-end subroutine map_vectors
-
-
-
-subroutine map_connectivity
-implicit none
-
-allocate(cellsOnEdgeNew(TWONew,nEdgesNew))
-allocate(boundaryEdgeNew(nVertLevelsNew,nEdgesNew))
-allocate(flipVerticesOnEdgeOrdering(nEdgesNew))
-cellsOnEdgeNew(:,:) = 0
-boundaryEdgeNew(:,:) = 0
-flipVerticesOnEdgeOrdering(:) = 0
-do iEdge=1,nEdges
-if(edgeMap(iEdge).eq.0) cycle
-iEdgeNew = edgeMap(iEdge)
-iCell1 = cellsOnEdge(1,iEdge)
-iCell2 = cellsOnEdge(2,iEdge)
-iCell1New = cellMap(iCell1)
-iCell2New = cellMap(iCell2)
-cellsOnEdgeNew(1,iEdgeNew) = iCell1New
-cellsOnEdgeNew(2,iEdgeNew) = iCell2New
-if(iCell1New.eq.0.or.iCell2New.eq.0) boundaryEdgeNew(:,iEdgeNew) = 1
-if(iCell1New.eq.0.and.iCell2New.eq.0) stop &quot;cellsOnEdge&quot;
-if(iCell1New.eq.0) then
-    cellsOnEdgeNew(1,iEdgeNew) = iCell2New
-    cellsOnEdgeNew(2,iEdgeNew) = iCell1New
-    flipVerticesOnEdgeOrdering(iEdgeNew) = 1
-endif
-enddo
-deallocate(cellsOnEdge)
-
-allocate(verticesOnEdgeNew(TWONew,nEdgesNew))
-allocate(boundaryVertexNew(nVertLevelsNew,nVerticesNew))
-verticesOnEdgeNew(:,:) = 0
-boundaryVertexNew(:,:) = 0
-do iEdge=1,nEdges
-if(edgeMap(iEdge).eq.0) cycle
-iEdgeNew = edgeMap(iEdge)
-iVertex1 = VerticesOnEdge(1,iEdge)
-iVertex2 = VerticesOnEdge(2,iEdge)
-iVertex1New = vertexMap(iVertex1)
-iVertex2New = vertexMap(iVertex2)
-if(iVertex1New.eq.0.or.iVertex2New.eq.0) stop &quot;verticesOnEdge&quot;
-if(flipVerticesOnEdgeOrdering(iEdgeNew).eq.0) then
-  verticesOnEdgeNew(1,iEdgeNew) = iVertex1New
-  verticesOnEdgeNew(2,iEdgeNew) = iVertex2New
-else
-  verticesOnEdgeNew(1,iEdgeNew) = iVertex2New
-  verticesOnEdgeNew(2,iEdgeNew) = iVertex1New
-endif
-if(boundaryEdgeNew(1,iEdgeNew).eq.1) then
-    boundaryVertexNew(:,iVertex1New)=1
-    boundaryVertexNew(:,iVertex2New)=1
-endif
-enddo
-deallocate(verticesOnEdge)
-
-allocate(nEdgesOnEdgeNew(nEdgesNew))
-allocate(edgesOnEdgeNew(maxEdges2,nEdgesNew))
-allocate(weightsOnEdgeNew(maxEdges2,nEdgesNew))
-nEdgesOnEdgeNew(:) = 0
-edgesOnEdgeNew(:,:) = 0
-weightsOnEdgeNew(:,:) = 0.0
-do iEdge=1,nEdges
-if(edgeMap(iEdge).eq.0) cycle
-iEdgeNew = edgeMap(iEdge)
-if(boundaryEdgeNew(1,iEdgeNew).eq.1) then
-    nEdgesOnEdgeNew(iEdgeNew) = 0
-    edgesOnEdgeNew(:,iEdgeNew) = 0
-    weightsOnEdgeNew(:,iEdgeNew) = 0.0
-else
-    nEdgesOnEdgeNew(iEdgeNew) = nEdgesOnEdge(iEdge)
-    do i=1,nEdgesOnEdgeNew(iEdgeNew)
-    jEdge = edgesOnEdge(i,iEdge)
-    jEdgeNew = edgeMap(jEdge)
-    if(jEdgeNew.eq.0) stop &quot;jEdgeNew&quot;
-    edgesOnEdgeNew(i,iEdgeNew)=jEdgeNew
-    weightsOnEdgeNew(i,iEdgeNew) = weightsOnEdge(i,iEdge)
-    enddo
-endif
-enddo
-deallocate(nEdgesOnEdge)
-deallocate(edgesOnEdge)
-deallocate(weightsOnEdge)
-
-allocate(cellsOnCellNew(maxEdges,nCellsNew))
-allocate(nEdgesOnCellNew(nCellsNew))
-cellsOnCellNew = 0
-nEdgesOnCellNew = 0
-do iCell=1,nCells
-if(cellMap(iCell).eq.0) cycle
-iCellNew = cellMap(iCell)
-nEdgesOnCellNew(iCellNew)=nEdgesOnCell(iCell)
-do i=1,nEdgesOnCellNew(iCellNew)
-j = cellsOnCell(i,iCell)
-jNew = cellMap(j)
-cellsOnCellNew(i,iCellNew) = jNew
-enddo
-enddo
-deallocate(cellsOnCell)
-deallocate(nEdgesOnCell)
-
-allocate(edgesOnCellNew(maxEdgesNew,nCellsNew))
-edgesOnCellNew(:,:) = 0
-do iCell=1,nCells
-if(cellMap(iCell).eq.0) cycle
-iCellNew = cellMap(iCell)
-do i=1,nEdgesOnCellNew(iCellNew)
-j = edgesOnCell(i,iCell)
-jNew = edgeMap(j)
-if(jNew.eq.0) stop &quot;edgesOnCell&quot;
-edgesOnCellNew(i,iCellNew) = jNew
-enddo
-enddo
-deallocate(edgesOnCell)
-
-allocate(verticesOnCellNew(maxEdgesNew,nCellsNew))
-verticesOnCellNew(:,:)=0
-do iCell=1,nCells
-if(cellMap(iCell).eq.0) cycle
-iCellNew = cellMap(iCell)
-do i=1,nEdgesOnCellNew(iCellNew)
-j=verticesOnCell(i,iCell)
-jNew = vertexMap(j)
-if(jNew.eq.0) stop &quot;verticesOnCell&quot;
-verticesOnCellNew(i,iCellNew) = jNew
-enddo
-enddo
-deallocate(verticesOnCell)
-
-allocate(cellsOnVertexNew(vertexDegreeNew,nVerticesNew))
-allocate(kiteAreasOnVertexNew(vertexDegreeNew,nVerticesNew))
-cellsOnVertexNew = 0
-kiteAreasOnVertexNew = 0
-do iVertex=1,nVertices
-if(vertexMap(iVertex).eq.0) cycle
-iVertexNew = vertexMap(iVertex)
-do i=1,vertexDegree
-j=cellsOnVertex(i,iVertex)
-jNew=cellMap(j)
-if(jNew.eq.0) then
-    kiteAreasOnVertexNew(i,iVertexNew)=0
-else
-    kiteAreasOnVertexNew(i,iVertexNew)=kiteAreasOnVertex(i,iVertex)
-endif
-cellsOnVertexNew(i,iVertexNew)=jNew
-enddo
-enddo
-deallocate(cellsOnVertex)
-deallocate(kiteAreasOnVertex)
-
-areaTriangleNew = 0
-do iVertex=1,nVerticesNew
-do i=1,vertexDegree
-areaTriangleNew(iVertex) = areaTriangleNew(iVertex) + kiteAreasOnVertexNew(i,iVertex)
-enddo
-enddo
-
-allocate(edgesOnVertexNew(vertexDegreeNew, nVerticesNew))
-edgesOnVertexNew = 0
-do iVertex=1,nVertices
-if(vertexMap(iVertex).eq.0) cycle
-iVertexNew = vertexMap(iVertex)
-do i=1,vertexDegree
-j=edgesOnVertex(i,iVertex)
-jNew=edgeMap(j)
-edgesOnVertexNew(i,iVertexNew)=jNew
-enddo
-enddo
-deallocate(edgesOnVertex)
-
-! find normals
-normalsNew = 0.0
-do iEdge=1,nEdgesNew
-cell1 = cellsOnEdgeNew(1,iEdge)
-cell2 = cellsOnEdgeNew(2,iEdge)
-if(cell1.eq.0.or.cell2.eq.0) cycle
-c1(1) = xCellNew(cell1); c1(2) = yCellNew(cell1); c1(3) = zCellNew(cell1)
-c2(1) = xCellNew(cell2); c2(2) = yCellNew(cell2); c2(3) = zCellNew(cell2)
-distance = sqrt( (c1(1)-c2(1))**2 + (c1(2)-c2(2))**2 + (c1(3)-c2(3))**2 )
-
-if(on_a_sphere.eq.'YES              ') then
-    normalsNew(1,iEdge) = c2(1) - c1(1)
-    normalsNew(2,iEdge) = c2(2) - c1(2)
-    normalsNew(3,iEdge) = c2(3) - c1(3)
-    distance = sqrt( (c1(1)-c2(1))**2 + (c1(2)-c2(2))**2 + (c1(3)-c2(3))**2 )
-    normalsNew(:,iEdge) = normalsNew(:,iEdge) / distance
-else
-    if(distance.gt.0.5*Lx) then
-        write(6,*) ' periodic edge ', iEdge, distance
-        write(6,10) '          c1   ', c1(:)
-        write(6,10) '          c2   ', c2(:)
-        r = c2(1) - c1(1)
-        if(r.gt.0) c2(1) = c2(1) - Lx
-        if(r.lt.0) c2(1) = c2(1) + Lx
-        distance = sqrt( (c1(1)-c2(1))**2 + (c1(2)-c2(2))**2 + (c1(3)-c2(3))**2 )
-        write(6,*) ' periodic edge fix ', iEdge, r, distance
-    endif
-    normalsNew(1,iEdge) = c2(1) - c1(1)
-    normalsNew(2,iEdge) = c2(2) - c1(2)
-    normalsNew(3,iEdge) = c2(3) - c1(3)
-    distance = sqrt( (c1(1)-c2(1))**2 + (c1(2)-c2(2))**2 + (c1(3)-c2(3))**2 )
-    normalsNew(:,iEdge) = normalsNew(:,iEdge) / distance
-endif
-enddo
-10 format(a20,3e15.5)
-
-end subroutine map_connectivity
-
-
-subroutine get_dz
-integer k
-
-  dz( 1) = 1001.244   !   5.006218       10.01244
-  dz( 2) = 1011.258   !   15.06873       20.12502
-  dz( 3) = 1031.682   !   25.28342       30.44183
-  dz( 4) = 1063.330   !   35.75848       41.07513
-  dz( 5) = 1107.512   !   46.61269       52.15025
-  dz( 6) = 1166.145   !   57.98098       63.81171
-  dz( 7) = 1241.928   !   70.02135       76.23099
-  dz( 8) = 1338.612   !   82.92405       89.61711
-  dz( 9) = 1461.401   !   96.92412       104.2311
-  dz(10) = 1617.561   !   112.3189       120.4067
-  dz(11) = 1817.368   !   129.4936       138.5804
-  dz(12) = 2075.558   !   148.9582       159.3360
-  dz(13) = 2413.680   !   171.4044       183.4728
-  dz(14) = 2863.821   !   197.7919       212.1110
-  dz(15) = 3474.644   !   229.4842       246.8575
-  dz(16) = 4320.857   !   268.4617       290.0660
-  dz(17) = 5516.812   !   317.6501       345.2342
-  dz(18) = 7230.458   !   381.3865       417.5388
-  dz(19) = 9674.901   !   465.9133       514.2878
-  dz(20) = 13003.92   !   579.3074       644.3270
-  dz(21) = 17004.89   !   729.3514       814.3759
-  dz(22) = 20799.33   !   918.3725       1022.369
-  dz(23) = 23356.94   !   1139.154       1255.939
-  dz(24) = 24527.19   !   1378.574       1501.210
-  dz(25) = 24898.04   !   1625.701       1750.191
-  dz(26) = 24983.22   !   1875.107       2000.023
-  dz(27) = 24997.87   !   2125.012       2250.002
-  dz(28) = 24999.79   !   2375.000       2500.000
-  dz(29) = 24999.98   !   2625.000       2749.999
-  dz(30) = 25000.00   !   2874.999       2999.999
-  dz(31) = 25000.00   !   3124.999       3249.999
-  dz(32) = 25000.00   !   3374.999       3499.999
-  dz(33) = 25000.00   !   3624.999       3749.999
-  dz(34) = 25000.00   !   3874.999       3999.999
-  dz(35) = 25000.00   !   4124.999       4249.999
-  dz(36) = 25000.00   !   4374.999       4499.999
-  dz(37) = 25000.00   !   4624.999       4749.999
-  dz(38) = 25000.00   !   4874.999       4999.999
-  dz(39) = 25000.00   !   5124.999       5249.999
-  dz(40) = 25000.00   !   5374.999       5499.999
-
-  dz = dz / 100.0
-
-  write(6,*)
-  do k=1,40
-    write(6,*) k,dz(k)
-  enddo
-  write(6,*)
-
-end subroutine get_dz
-end program map_to_basin

Modified: branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh
===================================================================
--- branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh        2012-03-15 17:18:06 UTC (rev 1648)
+++ branches/ocean_projects/ocean_test_cases_staging/ocean/baroclinic_channel/makeMeshes.sh        2012-03-15 18:59:24 UTC (rev 1649)
@@ -2,7 +2,7 @@
 
 ########################################################################################
 ## Change the horizontal spacings, vertical levels, and cells in the x direction here ##
-## To start, grids are periodic in the x direction. This may change later                          ##
+## To start, grids are periodic in the x direction. This may change later             ##
 ########################################################################################
 SPACINGS=&quot;1000 4000 10000&quot;
 VERTLEVS=&quot;20&quot;
@@ -175,6 +175,7 @@
 
                 ln -s ${TCNAME}_${NAME}.grid.nc grid.nc
 
+                mkdir -p dx
                 ./map &gt; /dev/null
 
                 unlink grid.nc
@@ -201,7 +202,7 @@
                                 for PROC in $PROCS
                                 do
 
-                                        RUN_NAME=${NAME}_${VERTLEV}levs/${TIME_STEPPER}_${TIME_STEP}_${PROC}procs
+                                        RUN_NAME=${NAME}_${VERTLEV}levs/${TIME_STEPPER}_${TIME_STEP}/${PROC}procs
 
                                         mkdir -p ${RUN_NAME}
 
@@ -210,6 +211,8 @@
                                         ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info ${RUN_NAME}/graph.info
                                         ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.graph.info.part.${PROC} ${RUN_NAME}/graph.info.part.${PROC}
                                         ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/${TCNAME}_${NAME}_${VERTLEV}levs.grid.nc ${RUN_NAME}/grid.nc
+                                        ln -f -s ${CUR_DIR}/${NAME}_${VERTLEV}levs/dx ${RUN_NAME}/dx
+#                                        cp -R dx ${RUN_NAME}/dx
 
                                         ## Copy executable to run directory
                                         if [ $# -ge 1  ]; then
@@ -244,11 +247,13 @@
                 done
 
                 mv ${TCNAME}_${NAME}_${VERTLEV}levs* ${NAME}_${VERTLEV}levs/.
+                mv dx ${NAME}_${VERTLEV}levs/.
         done
 
         rm map
 done
 
+rm -rf dx
 rm  MPAS-namelist.input.template
 rm ${TCNAME}*
 rm fort.*

</font>
</pre>