From c2ecca505e988d6312cd88bd67ecf4a2d3f5504d Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Tue, 19 Sep 2017 16:07:45 -0800
Subject: [PATCH 1/8] Turning off the OBC tracer advection for now.

- It will come back with tracers on segments.
---
 src/tracer/MOM_tracer_advect.F90 | 68 ++++++++++++++++----------------
 1 file changed, 35 insertions(+), 33 deletions(-)

diff --git a/src/tracer/MOM_tracer_advect.F90 b/src/tracer/MOM_tracer_advect.F90
index 37b3e70a34..42c3ac6bbb 100644
--- a/src/tracer/MOM_tracer_advect.F90
+++ b/src/tracer/MOM_tracer_advect.F90
@@ -523,22 +523,23 @@ subroutine advect_x(Tr, hprev, uhr, uh_neglect, OBC, domore_u, ntr, Idt, &
           endif
         endif
       enddo
-    endif
-    if (OBC%open_u_BCs_exist_globally) then
-      do n=1,OBC%number_of_segments
-        if (OBC%segment(n)%specified) cycle
-        if (OBC%segment(n)%is_E_or_W) then
-          I = OBC%segment(n)%HI%IsdB
-          if (j >= OBC%segment(n)%HI%jsd .and. j<= OBC%segment(n)%HI%jed) then
-            do m=1,ntr
-              if (associated(Tr(m)%OBC_in_u)) then
-                uhh(I) = uhr(I,j,k)
-                flux_x(I,m) = uhh(I)*Tr(m)%OBC_in_u(I,j,k)
-              else ; flux_x(I,m) = uhh(I)*Tr(m)%OBC_inflow_conc ; endif
-            enddo
-          endif
-        endif
-      enddo
+!   endif
+    ! Not yet...
+!   if (OBC%open_u_BCs_exist_globally) then
+!     do n=1,OBC%number_of_segments
+!       if (OBC%segment(n)%specified) cycle
+!       if (OBC%segment(n)%is_E_or_W) then
+!         I = OBC%segment(n)%HI%IsdB
+!         if (j >= OBC%segment(n)%HI%jsd .and. j<= OBC%segment(n)%HI%jed) then
+!           do m=1,ntr
+!             if (associated(Tr(m)%OBC_in_u)) then
+!               uhh(I) = uhr(I,j,k)
+!               flux_x(I,m) = uhh(I)*Tr(m)%OBC_in_u(I,j,k)
+!             else ; flux_x(I,m) = uhh(I)*Tr(m)%OBC_inflow_conc ; endif
+!           enddo
+!         endif
+!       endif
+!     enddo
     endif ; endif ; endif
 
     ! Calculate new tracer concentration in each cell after accounting
@@ -816,23 +817,24 @@ subroutine advect_y(Tr, hprev, vhr, vh_neglect, OBC, domore_v, ntr, Idt, &
           endif
         endif
       enddo
-    endif
-    if (OBC%open_v_BCs_exist_globally) then
-      do n=1,OBC%number_of_segments
-        if (OBC%segment(n)%specified) cycle
-        if (OBC%segment(n)%is_N_or_S) then
-          if (J >= OBC%segment(n)%HI%JsdB .and. J<= OBC%segment(n)%HI%JedB) then
-            do i = OBC%segment(n)%HI%isd,OBC%segment(n)%HI%ied
-              do m=1,ntr
-                if (associated(Tr(m)%OBC_in_v)) then
-                  vhh(i,J) = vhr(i,J,k)
-                  flux_y(i,m,J) = vhh(i,J)*Tr(m)%OBC_in_v(i,J,k)
-                else ; flux_y(i,m,J) = vhh(i,J)*Tr(m)%OBC_inflow_conc ; endif
-              enddo
-            enddo
-          endif
-        endif
-      enddo
+!   endif
+! Coming soon...
+!   if (OBC%open_v_BCs_exist_globally) then
+!     do n=1,OBC%number_of_segments
+!       if (OBC%segment(n)%specified) cycle
+!       if (OBC%segment(n)%is_N_or_S) then
+!         if (J >= OBC%segment(n)%HI%JsdB .and. J<= OBC%segment(n)%HI%JedB) then
+!           do i = OBC%segment(n)%HI%isd,OBC%segment(n)%HI%ied
+!             do m=1,ntr
+!               if (associated(Tr(m)%OBC_in_v)) then
+!                 vhh(i,J) = vhr(i,J,k)
+!                 flux_y(i,m,J) = vhh(i,J)*Tr(m)%OBC_in_v(i,J,k)
+!               else ; flux_y(i,m,J) = vhh(i,J)*Tr(m)%OBC_inflow_conc ; endif
+!             enddo
+!           enddo
+!         endif
+!       endif
+!     enddo
     endif ; endif ; endif
   else ! not domore_v.
     do i=is,ie ; vhh(i,J) = 0.0 ; enddo

From a02220e247f5416610c91c32588a4fd43fc95a49 Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Tue, 19 Sep 2017 17:00:06 -0800
Subject: [PATCH 2/8] Setting h outside is needed for ALE regridding...

---
 src/core/MOM_open_boundary.F90 | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/src/core/MOM_open_boundary.F90 b/src/core/MOM_open_boundary.F90
index 9b2c5d0739..31c9f2d582 100644
--- a/src/core/MOM_open_boundary.F90
+++ b/src/core/MOM_open_boundary.F90
@@ -1647,6 +1647,33 @@ subroutine set_tracer_data(OBC, tv, h, G, PF, tracer_Reg)
     enddo
   endif
 
+  do n=1,OBC%number_of_segments
+    segment => OBC%segment(n)
+    if (.not. segment%on_pe) cycle
+
+    if (segment%direction == OBC_DIRECTION_E) then
+      I=segment%HI%IsdB
+      do k=1,G%ke ;  do j=segment%HI%jsd,segment%HI%jed
+        h(i+1,j,k) = h(i,j,k)
+      enddo; enddo
+    elseif (segment%direction == OBC_DIRECTION_W) then
+      I=segment%HI%IsdB
+      do k=1,G%ke ;  do j=segment%HI%jsd,segment%HI%jed
+        h(i,j,k) = h(i+1,j,k)
+      enddo; enddo
+    elseif (segment%direction == OBC_DIRECTION_N) then
+      J=segment%HI%JsdB
+      do k=1,G%ke ;  do i=segment%HI%isd,segment%HI%ied
+        h(i,j+1,k) = h(i,j,k)
+      enddo; enddo
+    elseif (segment%direction == OBC_DIRECTION_S) then
+      J=segment%HI%JsdB
+      do k=1,G%ke ;  do i=segment%HI%isd,segment%HI%ied
+        h(i,j,k) = h(i,j+1,k)
+      enddo; enddo
+    endif
+  enddo
+
 end subroutine set_tracer_data
 
 function lookup_seg_field(OBC_seg,field)

From e8edc15ea3a5c6dce62c5d42cd73e61708fac722 Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Mon, 25 Sep 2017 16:28:05 -0800
Subject: [PATCH 3/8] *Mask out the land outside of open boundaries.

- Changes some answers of problems with OBCs.
---
 src/core/MOM_open_boundary.F90 | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/core/MOM_open_boundary.F90 b/src/core/MOM_open_boundary.F90
index 9f06838d4d..7463f75161 100644
--- a/src/core/MOM_open_boundary.F90
+++ b/src/core/MOM_open_boundary.F90
@@ -1116,7 +1116,7 @@ end subroutine open_boundary_impose_normal_slope
 !! Also adjust u- and v-point cell area on specified open boundaries.
 subroutine open_boundary_impose_land_mask(OBC, G, areaCu, areaCv)
   type(ocean_OBC_type),              pointer       :: OBC !< Open boundary control structure
-  type(dyn_horgrid_type),            intent(in)    :: G !< Ocean grid structure
+  type(dyn_horgrid_type),            intent(inout) :: G !< Ocean grid structure
   real, dimension(SZIB_(G),SZJ_(G)), intent(inout) :: areaCu !< Area of a u-cell (m2)
   real, dimension(SZI_(G),SZJB_(G)), intent(inout) :: areaCv !< Area of a u-cell (m2)
   ! Local variables
@@ -1134,12 +1134,22 @@ subroutine open_boundary_impose_land_mask(OBC, G, areaCu, areaCv)
       I=segment%HI%IsdB
       do j=segment%HI%jsd,segment%HI%jed
         if (G%mask2dCu(I,j) == 0) OBC%segnum_u(I,j) = OBC_NONE
+        if (segment%direction == OBC_DIRECTION_W) then
+          G%mask2dT(i,j) = 0
+        else
+          G%mask2dT(i+1,j) = 0
+        endif
       enddo
     else
       ! Sweep along v-segments and delete the OBC for blocked points.
       J=segment%HI%JsdB
       do i=segment%HI%isd,segment%HI%ied
         if (G%mask2dCv(i,J) == 0) OBC%segnum_v(i,J) = OBC_NONE
+        if (segment%direction == OBC_DIRECTION_S) then
+          G%mask2dT(i,j) = 0
+        else
+          G%mask2dT(i,j+1) = 0
+        endif
       enddo
     endif
   enddo

From 6c05467d24f1eaf9595e76fe3871d7e8785680c2 Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Mon, 25 Sep 2017 16:54:00 -0800
Subject: [PATCH 4/8] Mask out those outside h points again.

---
 src/core/MOM_open_boundary.F90 | 52 +++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/src/core/MOM_open_boundary.F90 b/src/core/MOM_open_boundary.F90
index 7463f75161..153b901a42 100644
--- a/src/core/MOM_open_boundary.F90
+++ b/src/core/MOM_open_boundary.F90
@@ -1643,32 +1643,32 @@ subroutine set_tracer_data(OBC, tv, h, G, PF, tracer_Reg)
     enddo
   endif
 
-  do n=1,OBC%number_of_segments
-    segment => OBC%segment(n)
-    if (.not. segment%on_pe) cycle
-
-    if (segment%direction == OBC_DIRECTION_E) then
-      I=segment%HI%IsdB
-      do k=1,G%ke ;  do j=segment%HI%jsd,segment%HI%jed
-        h(i+1,j,k) = h(i,j,k)
-      enddo; enddo
-    elseif (segment%direction == OBC_DIRECTION_W) then
-      I=segment%HI%IsdB
-      do k=1,G%ke ;  do j=segment%HI%jsd,segment%HI%jed
-        h(i,j,k) = h(i+1,j,k)
-      enddo; enddo
-    elseif (segment%direction == OBC_DIRECTION_N) then
-      J=segment%HI%JsdB
-      do k=1,G%ke ;  do i=segment%HI%isd,segment%HI%ied
-        h(i,j+1,k) = h(i,j,k)
-      enddo; enddo
-    elseif (segment%direction == OBC_DIRECTION_S) then
-      J=segment%HI%JsdB
-      do k=1,G%ke ;  do i=segment%HI%isd,segment%HI%ied
-        h(i,j,k) = h(i,j+1,k)
-      enddo; enddo
-    endif
-  enddo
+! do n=1,OBC%number_of_segments
+!   segment => OBC%segment(n)
+!   if (.not. segment%on_pe) cycle
+
+!   if (segment%direction == OBC_DIRECTION_E) then
+!     I=segment%HI%IsdB
+!     do k=1,G%ke ;  do j=segment%HI%jsd,segment%HI%jed
+!       h(i+1,j,k) = h(i,j,k)
+!     enddo; enddo
+!   elseif (segment%direction == OBC_DIRECTION_W) then
+!     I=segment%HI%IsdB
+!     do k=1,G%ke ;  do j=segment%HI%jsd,segment%HI%jed
+!       h(i,j,k) = h(i+1,j,k)
+!     enddo; enddo
+!   elseif (segment%direction == OBC_DIRECTION_N) then
+!     J=segment%HI%JsdB
+!     do k=1,G%ke ;  do i=segment%HI%isd,segment%HI%ied
+!       h(i,j+1,k) = h(i,j,k)
+!     enddo; enddo
+!   elseif (segment%direction == OBC_DIRECTION_S) then
+!     J=segment%HI%JsdB
+!     do k=1,G%ke ;  do i=segment%HI%isd,segment%HI%ied
+!       h(i,j,k) = h(i,j+1,k)
+!     enddo; enddo
+!   endif
+! enddo
 
 end subroutine set_tracer_data
 

From 8d33a65330ec8b679b83ae3761f9731bc6e02733 Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Tue, 26 Sep 2017 08:59:14 -0800
Subject: [PATCH 5/8] *Fix tracer upstream OBC

-Changes answers for ESMG seamount cases.
---
 src/tracer/MOM_tracer_advect.F90 | 40 +++++++++++++++++++++++++++-----
 1 file changed, 34 insertions(+), 6 deletions(-)

diff --git a/src/tracer/MOM_tracer_advect.F90 b/src/tracer/MOM_tracer_advect.F90
index 728d838182..9293940109 100644
--- a/src/tracer/MOM_tracer_advect.F90
+++ b/src/tracer/MOM_tracer_advect.F90
@@ -532,9 +532,23 @@ subroutine advect_x(Tr, hprev, uhr, uh_neglect, OBC, domore_u, ntr, Idt, &
           if (j >= OBC%segment(n)%HI%jsd .and. j<= OBC%segment(n)%HI%jed) then
             uhh(I) = uhr(I,j,k)
             do m=1,ntr
-              if (associated(OBC%segment(n)%tr_Reg%Tr(m)%t)) then
-                flux_x(I,m) = uhh(I)*OBC%segment(n)%tr_Reg%Tr(m)%t(I,j,k)
-              else ; flux_x(I,m) = uhh(I)*OBC%segment(n)%tr_Reg%Tr(m)%OBC_inflow_conc ; endif
+              if (OBC%segment(n)%direction == OBC_DIRECTION_E) then
+                if (uhh(I) > 0.0) then
+                  flux_x(I,m) = uhh(I)*Tr(m)%t(i,j,k)
+                else
+                  if (associated(OBC%segment(n)%tr_Reg%Tr(m)%t)) then
+                    flux_x(I,m) = uhh(I)*OBC%segment(n)%tr_Reg%Tr(m)%t(I,j,k)
+                  else ; flux_x(I,m) = uhh(I)*OBC%segment(n)%tr_Reg%Tr(m)%OBC_inflow_conc ; endif
+                endif
+              else ! West
+                if (uhh(I) < 0.0) then
+                  flux_x(I,m) = uhh(I)*Tr(m)%t(i+1,j,k)
+                else
+                  if (associated(OBC%segment(n)%tr_Reg%Tr(m)%t)) then
+                    flux_x(I,m) = uhh(I)*OBC%segment(n)%tr_Reg%Tr(m)%t(I,j,k)
+                  else ; flux_x(I,m) = uhh(I)*OBC%segment(n)%tr_Reg%Tr(m)%OBC_inflow_conc ; endif
+                endif
+              endif
             enddo
           endif
         endif
@@ -827,9 +841,23 @@ subroutine advect_y(Tr, hprev, vhr, vh_neglect, OBC, domore_v, ntr, Idt, &
             do i = OBC%segment(n)%HI%isd,OBC%segment(n)%HI%ied
               vhh(i,J) = vhr(i,J,k)
               do m=1,ntr
-                if (associated(OBC%segment(n)%tr_Reg%Tr(m)%t)) then
-                  flux_y(i,m,J) = vhh(i,J)*OBC%segment(n)%tr_Reg%Tr(m)%t(i,J,k)
-                else ; flux_y(i,m,J) = vhh(i,J)*OBC%segment(n)%tr_Reg%Tr(m)%OBC_inflow_conc ; endif
+                if (OBC%segment(n)%direction == OBC_DIRECTION_N) then
+                  if (vhh(i,J) > 0.0) then
+                    flux_y(i,m,J) = vhh(i,J)*Tr(m)%t(i,j,k)
+                  else
+                    if (associated(OBC%segment(n)%tr_Reg%Tr(m)%t)) then
+                      flux_y(i,m,J) = vhh(i,J)*OBC%segment(n)%tr_Reg%Tr(m)%t(i,J,k)
+                    else ; flux_y(i,m,J) = vhh(i,J)*OBC%segment(n)%tr_Reg%Tr(m)%OBC_inflow_conc ; endif
+                  endif
+                else ! South
+                  if (vhh(i,J) < 0.0) then
+                    flux_y(i,m,J) = vhh(i,J)*Tr(m)%t(i,j,k)
+                  else
+                    if (associated(OBC%segment(n)%tr_Reg%Tr(m)%t)) then
+                      flux_y(i,m,J) = vhh(i,J)*OBC%segment(n)%tr_Reg%Tr(m)%t(i,J,k)
+                    else ; flux_y(i,m,J) = vhh(i,J)*OBC%segment(n)%tr_Reg%Tr(m)%OBC_inflow_conc ; endif
+                  endif
+                endif
               enddo
             enddo
           endif

From c6d5a6e4df1cdda493a7bbf29fff307bb0915018 Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Wed, 27 Sep 2017 09:20:35 -0800
Subject: [PATCH 6/8] Doxygen of generic tracer

---
 .../MOM_state_initialization.F90              |   7 +-
 src/tracer/MOM_generic_tracer.F90             | 369 ++++++------------
 2 files changed, 124 insertions(+), 252 deletions(-)

diff --git a/src/initialization/MOM_state_initialization.F90 b/src/initialization/MOM_state_initialization.F90
index 3d77e1a0c4..696f612e28 100644
--- a/src/initialization/MOM_state_initialization.F90
+++ b/src/initialization/MOM_state_initialization.F90
@@ -1629,9 +1629,10 @@ subroutine initialize_sponges_file(G, GV, use_temperature, tv, param_file, CSp,
   type(param_file_type),   intent(in) :: param_file !< A structure to parse for run-time parameters.
   type(sponge_CS),         pointer    :: CSp  !< A pointer that is set to point to the control
                                               !! structure for this module (in layered mode).
-  type(ALE_sponge_CS),         pointer    :: ALE_CSp  !< A pointer that is set to point to the control
-                                                      !! structure for this module (in ALE mode).
-  type(time_type),         intent(in) :: Time
+  type(ALE_sponge_CS),     pointer    :: ALE_CSp  !< A pointer that is set to point to the control
+                                                  !! structure for this module (in ALE mode).
+  type(time_type),         intent(in) :: Time !< Time at the start of the run segment. Time_in
+                                              !! overrides any value set for Time.
 
 ! Local variables
   real, allocatable, dimension(:,:,:) :: eta ! The target interface heights, in m.
diff --git a/src/tracer/MOM_generic_tracer.F90 b/src/tracer/MOM_generic_tracer.F90
index 891f29dbbd..d905f3f307 100644
--- a/src/tracer/MOM_generic_tracer.F90
+++ b/src/tracer/MOM_generic_tracer.F90
@@ -2,18 +2,6 @@ module MOM_generic_tracer
 
 ! This file is part of MOM6. See LICENSE.md for the license.
 
-!----------------------------------------------------------------
-! <CONTACT EMAIL="Niki.Zadeh@noaa.gov"> Niki Zadeh
-! </CONTACT>
-!
-! <REVIEWER EMAIL="William.Cooke@noaa.gov"> William Cooke
-! </REVIEWER>
-!
-! <OVERVIEW>
-!  This module drives the generic version of tracers TOPAZ and CFC
-! </OVERVIEW>
-!----------------------------------------------------------------
-
 #include <MOM_memory.h>
 
 #ifdef _USE_GENERIC_TRACER
@@ -99,41 +87,20 @@ module MOM_generic_tracer
 
 contains
 
-  ! <SUBROUTINE NAME="register_MOM_generic_tracer">
-  !  <OVERVIEW>
-  !   Initialize phase I: Add the generic tracers
-  !  </OVERVIEW>
-  !  <DESCRIPTION>
-  !   This subroutine:
-  !     Initializes the generic tracer packages and adds their tracers to the list
-  !     Adds the tracers in the list of generic tracers to the set of MOM tracers (i.e., MOM-register them)
-  !     Register these tracers for restart
-  !  </DESCRIPTION>
-  !  <TEMPLATE>
-  !   call register_MOM_generic_tracer(G, param_file, CS, diag, tr_Reg, restart_CS)
-  !  </TEMPLATE>
-  ! </SUBROUTINE>
-
+  !> Initializes the generic tracer packages and adds their tracers to the list
+  !! Adds the tracers in the list of generic tracers to the set of MOM tracers (i.e., MOM-register them)
+  !! Register these tracers for restart
   function register_MOM_generic_tracer(HI, GV, param_file, CS, tr_Reg, restart_CS)
-    type(hor_index_type),       intent(in)   :: HI
-    type(verticalGrid_type),    intent(in)   :: GV   !< The ocean's vertical grid structure
+    type(hor_index_type),       intent(in)   :: HI         !< Horizontal index ranges
+    type(verticalGrid_type),    intent(in)   :: GV         !< The ocean's vertical grid structure
     type(param_file_type),      intent(in)   :: param_file !< A structure to parse for run-time parameters
-    type(MOM_generic_tracer_CS), pointer      :: CS
-    type(tracer_registry_type), pointer     :: tr_Reg
-    type(MOM_restart_CS),       pointer     :: restart_CS
-    ! This subroutine is used to register tracer fields and subroutines
-    ! to be used with MOM.
-    ! Arguments: G - The ocean's grid structure.
-    !  (in)      param_file - A structure indicating the open file to parse for
-    !                         model parameter values.
-    !  (in/out)  CS - A pointer that is set to point to the control structure
-    !                 for this module
-    !  (in)      diag - A structure that is used to regulate diagnostic output.
-    !  (in/out)  tr_Reg - A pointer that is set to point to the control structure
-    !                  for the tracer advection and diffusion module.
-    !  (in)      restart_CS - A pointer to the restart control structure.
-    logical :: register_MOM_generic_tracer
+    type(MOM_generic_tracer_CS), pointer     :: CS         !< Pointer to the control structure for this module
+    type(tracer_registry_type), pointer      :: tr_Reg     !< Pointer to the control structure for the tracer
+                                                           !! advection and diffusion module.
+    type(MOM_restart_CS),       pointer      :: restart_CS !< Pointer to the restart control structure.
 
+! Local variables
+    logical :: register_MOM_generic_tracer
 
     character(len=fm_string_len), parameter :: sub_name = 'register_MOM_generic_tracer'
     character(len=200) :: inputdir ! The directory where NetCDF input files are.
@@ -254,53 +221,33 @@ function register_MOM_generic_tracer(HI, GV, param_file, CS, tr_Reg, restart_CS)
     register_MOM_generic_tracer = .true.
   end function register_MOM_generic_tracer
 
-  ! <SUBROUTINE NAME="initialize_MOM_generic_tracer">
-  !  <OVERVIEW>
-  !   Initialize phase II:  Initialize required variables for generic tracers
-  !  </OVERVIEW>
-  !  <DESCRIPTION>
-  !   There are some steps of initialization that cannot be done in register_MOM_generic_tracer
-  !   This is the place and time to do them:
-  !       Set the grid mask and initial time for all generic tracers.
-  !       Diag_register them.
-  !       Z_diag_register them.
-  !  </DESCRIPTION>
-  !  <TEMPLATE>
-  !   call initialize_MOM_generic_tracer(restart, day, G, h, OBC, CS, sponge_CSp,ALE_sponge_CSp, diag_to_Z_CSp)
- ! </SUBROUTINE>
+  !>  Initialize phase II:  Initialize required variables for generic tracers
+  !!  There are some steps of initialization that cannot be done in register_MOM_generic_tracer
+  !!  This is the place and time to do them:
+  !!      Set the grid mask and initial time for all generic tracers.
+  !!      Diag_register them.
+  !!      Z_diag_register them.
+  !!
+  !!   This subroutine initializes the NTR tracer fields in tr(:,:,:,:)
+  !! and it sets up the tracer output.
   subroutine initialize_MOM_generic_tracer(restart, day, G, GV, h, param_file, diag, OBC, CS, &
                                           sponge_CSp, ALE_sponge_CSp,diag_to_Z_CSp)
-    logical,                               intent(in) :: restart
-    type(time_type), target,               intent(in) :: day
+    logical,                               intent(in) :: restart !< .true. if the fields have already been
+                                                                 !! read from a restart file.
+    type(time_type), target,               intent(in) :: day     !< Time of the start of the run.
     type(ocean_grid_type),                 intent(inout) :: G    !< The ocean's grid structure
     type(verticalGrid_type),               intent(in)    :: GV   !< The ocean's vertical grid structure
     real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h    !< Layer thicknesses, in H (usually m or kg m-2)
     type(param_file_type),                 intent(in) :: param_file !< A structure to parse for run-time parameters
-    type(diag_ctrl),               target, intent(in) :: diag
-    type(ocean_OBC_type),                  pointer    :: OBC
-    type(MOM_generic_tracer_CS),           pointer    :: CS
-    type(sponge_CS),                       pointer    :: sponge_CSp
-    type(ALE_sponge_CS),                   pointer    :: ALE_sponge_CSp
-    type(diag_to_Z_CS),                    pointer    :: diag_to_Z_CSp
-    !   This subroutine initializes the NTR tracer fields in tr(:,:,:,:)
-    ! and it sets up the tracer output.
-
-    ! Arguments: restart - .true. if the fields have already been read from
-    !                     a restart file.
-    !  (in)      day - Time of the start of the run.
-    !  (in)      G - The ocean's grid structure.
-    !  (in)      GV - The ocean's vertical grid structure.
-    !  (in)      h - Layer thickness, in m or kg m-2.
-    !  (in)      OBC - This open boundary condition type specifies whether, where,
-    !                  and what open boundary conditions are used.
-    !  (in/out)  CS - The control structure returned by a previous call to
-    !                 register_MOM_generic_tracer.
-    !  (in/out)  sponge_CSp - A pointer to the control structure for the sponges, if
-    !                         they are in use.  Otherwise this may be unassociated.
-    !  (in/out)  ALE_sponge_CSp - A pointer to the control structure for the ALE
-    !                 sponges, if they are in use.  Otherwise this may be unassociated
-    !  (in/out)  diag_to_Z_Csp - A pointer to the control structure for diagnostics
-    !                            in depth space.
+    type(diag_ctrl),               target, intent(in) :: diag    !< Regulates diagnostic output.
+    type(ocean_OBC_type),                  pointer    :: OBC     !< This open boundary condition type specifies whether,
+                                                                 !! where, and what open boundary conditions are used.
+    type(MOM_generic_tracer_CS),           pointer    :: CS      !< Pointer to the control structure for this module.
+    type(sponge_CS),                       pointer    :: sponge_CSp     !< Pointer to the control structure for the sponges.
+    type(ALE_sponge_CS),                   pointer    :: ALE_sponge_CSp !< Pointer  to the control structure for the
+                                                                        !! ALE sponges.
+    type(diag_to_Z_CS),                    pointer    :: diag_to_Z_CSp  !< A pointer to the control structure for diagnostics
+                                                                        !! in depth space.
 
     character(len=fm_string_len), parameter :: sub_name = 'initialize_MOM_generic_tracer'
     logical :: OK
@@ -480,62 +427,44 @@ subroutine initialize_MOM_generic_tracer(restart, day, G, GV, h, param_file, dia
 
   end subroutine initialize_MOM_generic_tracer
 
-  ! <SUBROUTINE NAME="MOM_generic_tracer_column_physics">
-  !  <OVERVIEW>
-  !   Column physics for generic tracers.
-  !  </OVERVIEW>
-  !  <DESCRIPTION>
-  !   This subroutine does:
-  !       Get the coupler values for generic tracers that exchange with atmosphere
-  !       Update generic tracer concentration fields from sources and sinks.
-  !       Vertically diffuse generic tracer concentration fields.
-  !       Update generic tracers from bottom and their bottom reservoir.
-  !  </DESCRIPTION>
-  !  <TEMPLATE>
-  !   call MOM_generic_tracer_column_physics(h_old, h_new, ea, eb, fluxes, dt, G, CS, tv, optics)
-  !  </TEMPLATE>
-  ! </SUBROUTINE>
-
+  !>  Column physics for generic tracers.
+  !!      Get the coupler values for generic tracers that exchange with atmosphere
+  !!      Update generic tracer concentration fields from sources and sinks.
+  !!      Vertically diffuse generic tracer concentration fields.
+  !!      Update generic tracers from bottom and their bottom reservoir.
+  !!
+  !!   This subroutine applies diapycnal diffusion and any other column
+  !! tracer physics or chemistry to the tracers from this file.
+  !! CFCs are relatively simple, as they are passive tracers. with only a surface
+  !! flux as a source.
   subroutine MOM_generic_tracer_column_physics(h_old, h_new, ea, eb, fluxes, Hml, dt, G, GV, CS, tv, optics, &
         evap_CFL_limit, minimum_forcing_depth)
     type(ocean_grid_type),                 intent(in) :: G    !< The ocean's grid structure
     type(verticalGrid_type),               intent(in) :: GV   !< The ocean's vertical grid structure
-    real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h_old, h_new, ea, eb
+  real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h_old !< Layer thickness before entrainment,
+                                                                !! in m or kg !m-2.
+  real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h_new !< Layer thickness after entrainment,
+                                                                !! in m or kg !m-2.
+  real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: ea    !< an array to which the amount of
+                                              !! fluid entrained from the layer !above during this
+                                              !! call will be added, in m or kg !m-2.
+  real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: eb    !< an array to which the amount of
+                                              !! fluid entrained from the layer !below during this
+                                              !! call will be added, in m or kg !m-2.
     type(forcing),                         intent(in) :: fluxes
     real, dimension(SZI_(G),SZJ_(G)),      intent(in) :: Hml  !< Mixed layer depth
     real,                                  intent(in) :: dt   !< The amount of time covered by this call, in s
-    type(MOM_generic_tracer_CS),           pointer    :: CS
+    type(MOM_generic_tracer_CS),           pointer    :: CS   !< Pointer to the control structure for this module.
     type(thermo_var_ptrs),                 intent(in) :: tv   !< A structure pointing to various thermodynamic variables
     type(optics_type),                     intent(in) :: optics
-    real,                        optional,intent(in)  :: evap_CFL_limit
-    real,                        optional,intent(in)  :: minimum_forcing_depth
-    !   This subroutine applies diapycnal diffusion and any other column
-    ! tracer physics or chemistry to the tracers from this file.
-    ! CFCs are relatively simple, as they are passive tracers. with only a surface
-    ! flux as a source.
-
-    ! Arguments: h_old -  Layer thickness before entrainment, in m or kg m-2.
-    !  (in)      h_new -  Layer thickness after entrainment, in m or kg m-2.
-    !  (in)      ea - an array to which the amount of fluid entrained
-    !                 from the layer above during this call will be
-    !                 added, in m or kg m-2.
-    !  (in)      eb - an array to which the amount of fluid entrained
-    !                 from the layer below during this call will be
-    !                 added, in m or kg m-2.
-    !  (in)      fluxes - A structure containing pointers to any possible
-    !                     forcing fields.  Unused fields have NULL ptrs.
-    !  (in)      dt - The amount of time covered by this call, in s.
-    !  (in)      G - The ocean's grid structure.
-    !  (in)      GV - The ocean's vertical grid structure.
-    !  (in)      CS - The control structure returned by a previous call to
-    !                 register_MOM_generic_tracer.
-    !  (in)      evap_CFL_limit - Limits how much water can be fluxed out of the top layer
-    !                             Stored previously in diabatic CS.
-    !  (in)      minimum_forcing_depth - The smallest depth over which fluxes can be applied
-    !                             Stored previously in diabatic CS.
-    !
+    real,                        optional,intent(in)  :: evap_CFL_limit !< Limits how much water can be fluxed out of
+                                                                        !! the top layer Stored previously in diabatic CS.
+    real,                        optional,intent(in)  :: minimum_forcing_depth !< The smallest depth over which fluxes
+                                                                        !!  can be applied Stored previously in diabatic CS.
     ! The arguments to this subroutine are redundant in that
     !     h_new[k] = h_old[k] + ea[k] - eb[k-1] + eb[k] - ea[k+1]
+
+! Local variables
     character(len=fm_string_len), parameter :: sub_name = 'MOM_generic_tracer_column_physics'
 
     type(g_tracer_type), pointer  :: g_tracer, g_tracer_next
@@ -660,46 +589,26 @@ subroutine MOM_generic_tracer_column_physics(h_old, h_new, ea, eb, fluxes, Hml,
 
   end subroutine MOM_generic_tracer_column_physics
 
-  ! <SUBROUTINE NAME="MOM_generic_tracer_stock">
-  !  <OVERVIEW>
-  !   Calculate the mass-weighted integral of tracer concentrations.
-  !  </OVERVIEW>
-  !  <DESCRIPTION>
-  !     This subroutine calculates mass-weighted integral on the PE either
-  !   of all available tracer concentrations, or of a tracer that is
-  !   being requested specifically, returning the number of stocks it has
-  !   calculated.
-  !  </DESCRIPTION>
-  !  <TEMPLATE>
-  !   ns = MOM_generic_tracer_stock(h, stocks, G, CS, names, units, stock_index)
-  !  </TEMPLATE>
-  ! </SUBROUTINE>
-
+  !> This subroutine calculates mass-weighted integral on the PE either
+  !! of all available tracer concentrations, or of a tracer that is
+  !! being requested specifically, returning the number of stocks it has
+  !! calculated. If the stock_index is present, only the stock corresponding
+  !! to that coded index is returned.
   function MOM_generic_tracer_stock(h, stocks, G, GV, CS, names, units, stock_index)
     type(ocean_grid_type),              intent(in)    :: G    !< The ocean's grid structure
     type(verticalGrid_type),            intent(in)    :: GV   !< The ocean's vertical grid structure
-    real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in)    :: h    !< Layer thicknesses, in H (usually m or kg m-2)
-    real, dimension(:),                 intent(out)   :: stocks
-    type(MOM_generic_tracer_CS),        pointer       :: CS
-    character(len=*), dimension(:),     intent(out)   :: names
-    character(len=*), dimension(:),     intent(out)   :: units
-    integer, optional,                  intent(in)    :: stock_index
-    integer                                           :: MOM_generic_tracer_stock
-  ! This function calculates the mass-weighted integral of all tracer stocks,
-  ! returning the number of stocks it has calculated.  If the stock_index
-  ! is present, only the stock corresponding to that coded index is returned.
-
-  ! Arguments: h - Layer thickness, in m or kg m-2.
-  !  (out)     stocks - the mass-weighted integrated amount of each tracer,
-  !                     in kg times concentration units.
-  !  (in)      G - The ocean's grid structure.
-  !  (in)      GV - The ocean's vertical grid structure.
-  !  (in)      CS - The control structure returned by a previous call to
-  !                 register_MOM_generic_tracer.
-  !  (out)     names - the names of the stocks calculated.
-  !  (out)     units - the units of the stocks calculated.
-  !  (in,opt)  stock_index - the coded index of a specific stock being sought.
-  ! Return value: the number of stocks calculated here.
+    real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h !< Layer thicknesses, in H (usually m or kg m-2)
+    real, dimension(:),                 intent(out)   :: stocks !< The mass-weighted integrated amount of each
+                                                                !! tracer, in kg times concentration units.
+    type(MOM_generic_tracer_CS),        pointer       :: CS     !< Pointer to the control structure for this module.
+    character(len=*), dimension(:),     intent(out)   :: names  !< The names of the stocks calculated.
+    character(len=*), dimension(:),     intent(out)   :: units  !< The units of the stocks calculated.
+    integer, optional,                  intent(in)    :: stock_index !< The coded index of a specific stock
+                                                                     !! being sought.
+    integer                                           :: MOM_generic_tracer_stock !< Return value, the
+                                                                     !! number of stocks calculated here.
+
+! Local variables
     type(g_tracer_type), pointer  :: g_tracer, g_tracer_next
     real, dimension(:,:,:,:), pointer   :: tr_field
     real, dimension(:,:,:), pointer     :: tr_ptr
@@ -746,46 +655,26 @@ function MOM_generic_tracer_stock(h, stocks, G, GV, CS, names, units, stock_inde
 
   end function MOM_generic_tracer_stock
 
-  ! <SUBROUTINE NAME="MOM_generic_tracer_min_max">
-  !  <OVERVIEW>
-  !   Find the min and max of tracer concentrations.
-  !  </OVERVIEW>
-  !  <DESCRIPTION>
-  !     This subroutine find the global min and max of either
-  !   of all available tracer concentrations, or of a tracer that is
-  !   being requested specifically, returning the number of tracers it has gone through.
-  !  </DESCRIPTION>
-  !  <TEMPLATE>
-  !   ns = MOM_generic_tracer_min_max(do_minmax, gmin, gmax, igmin, jgmin, kgmin, igmax, jgmax, kgmax , G, CS, names, units)
-  !  </TEMPLATE>
-  ! </SUBROUTINE>
-
+  !> This subroutine find the global min and max of either of all
+  !! available tracer concentrations, or of a tracer that is being
+  !! requested specifically, returning the number of tracers it has gone through.
   function MOM_generic_tracer_min_max(ind_start, got_minmax, gmin, gmax, xgmin, ygmin, zgmin, xgmax, ygmax, zgmax , G, CS, names, units)
     use mpp_utilities_mod, only: mpp_array_global_min_max
     integer,                            intent(in)    :: ind_start
     logical, dimension(:),              intent(out)   :: got_minmax
-    real, dimension(:),                 intent(out)   :: gmin,gmax
+    real, dimension(:),                 intent(out)   :: gmin   !< Global minimum of each tracer, in kg
+                                                                !! times concentration units.
+    real, dimension(:),                 intent(out)   :: gmax   !< Global maximum of each tracer, in kg
+                                                                !! times concentration units.
     real, dimension(:),                 intent(out)   :: xgmin, ygmin, zgmin, xgmax, ygmax, zgmax
-    type(ocean_grid_type),              intent(in)    :: G    !< The ocean's grid structure
-    type(MOM_generic_tracer_CS),       pointer       :: CS
-    character(len=*), dimension(:),     intent(out)   :: names
-    character(len=*), dimension(:),     intent(out)   :: units
-    integer                                           :: MOM_generic_tracer_min_max
-  ! This function calculates the mass-weighted integral of all tracer stocks,
-  ! returning the number of stocks it has calculated.  If the stock_index
-  ! is present, only the stock corresponding to that coded index is returned.
-
-  ! Arguments: h - Layer thickness, in m or kg m-2.
-  !  (out)     gmin , gmax - the global minimum and maximum of each tracer,
-  !                     in kg times concentration units.
-  !  (in)      G - The ocean's grid structure.
-  !  (in)      CS - The control structure returned by a previous call to
-  !                 register_MOM_generic_tracer.
-  !  (out)     names - the names of the stocks calculated.
-  !  (out)     units - the units of the stocks calculated.
-  !  (in,opt)  trace_index - the coded index of a specific tracer being sought.
-  ! Return value: the number of tracers done here.
-
+    type(ocean_grid_type),              intent(in)    :: G      !< The ocean's grid structure
+    type(MOM_generic_tracer_CS),        pointer       :: CS     !< Pointer to the control structure for this module.
+    character(len=*), dimension(:),     intent(out)   :: names  !< The names of the stocks calculated.
+    character(len=*), dimension(:),     intent(out)   :: units  !< The units of the stocks calculated.
+    integer                                           :: MOM_generic_tracer_min_max !< Return value, the
+                                                                !! number of tracers done here.
+
+! Local variables
     type(g_tracer_type), pointer  :: g_tracer, g_tracer_next
     real, dimension(:,:,:,:), pointer   :: tr_field
     real, dimension(:,:,:), pointer     :: tr_ptr
@@ -844,33 +733,19 @@ function MOM_generic_tracer_min_max(ind_start, got_minmax, gmin, gmax, xgmin, yg
   end function MOM_generic_tracer_min_max
 
 
-  ! <SUBROUTINE NAME="MOM_generic_tracer_surface_state">
-  !  <OVERVIEW>
-  !   Calculate the surface state and set coupler values
-  !  </OVERVIEW>
-  !  <DESCRIPTION>
-  !   This subroutine calculates the surface state and set coupler values for
-  !   those generic tracers that havd flux exchange with atmosphere.
-  !  </DESCRIPTION>
-  !  <TEMPLATE>
-  !   call MOM_generic_tracer_surface_state(state, h, G, CS)
-  !  </TEMPLATE>
-  ! </SUBROUTINE>
-
+  !> This subroutine calculates the surface state and sets coupler values for
+  !! those generic tracers that have flux exchange with atmosphere.
+  !!
+  !! This subroutine sets up the fields that the coupler needs to calculate the
+  !! CFC fluxes between the ocean and atmosphere.
   subroutine MOM_generic_tracer_surface_state(state, h, G, CS)
-    type(ocean_grid_type),                 intent(in) :: G    !< The ocean's grid structure
-    type(surface),                         intent(inout) :: state
+    type(ocean_grid_type),                 intent(in)    :: G    !< The ocean's grid structure
+    type(surface),                         intent(inout) :: state !< A structure containing fields that
+                                                                 !! describe the surface state of the ocean.
     real, dimension(SZI_(G),SZJ_(G),SZK_(G)), intent(in) :: h    !< Layer thicknesses, in H (usually m or kg m-2)
-    type(MOM_generic_tracer_CS),           pointer    :: CS
-    !   This subroutine sets up the fields that the coupler needs to calculate the
-    ! CFC fluxes between the ocean and atmosphere.
-    ! Arguments: state - A structure containing fields that describe the
-    !                    surface state of the ocean.
-    !  (in)      h - Layer thickness, in m.
-    !  (in)      G - The ocean's grid structure.
-    !  (in)      CS - The control structure returned by a previous call to
-    !                 register_MOM_generic_tracer.
+    type(MOM_generic_tracer_CS),           pointer       :: CS   !< Pointer to the control structure for this module.
 
+! Local variables
     real :: sosga
 
     character(len=fm_string_len), parameter :: sub_name = 'MOM_generic_tracer_surface_state'
@@ -948,13 +823,12 @@ subroutine MOM_generic_tracer_fluxes_accumulate(flux_tmp, weight)
 
   end subroutine MOM_generic_tracer_fluxes_accumulate
 
+  !> Copy the requested tracer into an array.
   subroutine MOM_generic_tracer_get(name,member,array, CS)
-    character(len=*),         intent(in)  :: name
-    character(len=*),         intent(in)  :: member
-    real, dimension(:,:,:),   intent(out) :: array
-    type(MOM_generic_tracer_CS), pointer :: CS
-    !  (in)      CS - The control structure returned by a previous call to
-    !                 register_MOM_generic_tracer.
+    character(len=*),         intent(in)  :: name   !< Name of requested tracer.
+    character(len=*),         intent(in)  :: member !< ??
+    real, dimension(:,:,:),   intent(out) :: array  !< Array filled by this routine.
+    type(MOM_generic_tracer_CS), pointer :: CS   !< Pointer to the control structure for this module.
 
     real, dimension(:,:,:),   pointer :: array_ptr
     character(len=fm_string_len), parameter :: sub_name = 'MOM_generic_tracer_get'
@@ -964,24 +838,9 @@ subroutine MOM_generic_tracer_get(name,member,array, CS)
 
   end subroutine MOM_generic_tracer_get
 
-  ! <SUBROUTINE NAME="end_MOM_generic_tracer">
-  !  <OVERVIEW>
-  !   Ends the generic tracer module
-  !  </OVERVIEW>
-  !  <DESCRIPTION>
-  !   Call the end for generic tracer module and deallocate all temp arrays
-  !  </DESCRIPTION>
-  !  <TEMPLATE>
-  !   call end_MOM_generic_tracer(CS)
-  !  </TEMPLATE>
-  ! </SUBROUTINE>
-
+  !> This subroutine deallocates the memory owned by this module.
   subroutine end_MOM_generic_tracer(CS)
-    type(MOM_generic_tracer_CS), pointer :: CS
-    !   This subroutine deallocates the memory owned by this module.
-    ! Argument: CS - The control structure returned by a previous call to
-    !                register_MOM_generic_tracer.
-    integer :: m
+    type(MOM_generic_tracer_CS), pointer :: CS   !< Pointer to the control structure for this module.
 
     call generic_tracer_end
 
@@ -991,4 +850,16 @@ subroutine end_MOM_generic_tracer(CS)
   end subroutine end_MOM_generic_tracer
 
 #endif /* _USE_GENERIC_TRACER */
+!----------------------------------------------------------------
+! <CONTACT EMAIL="Niki.Zadeh@noaa.gov"> Niki Zadeh
+! </CONTACT>
+!
+! <REVIEWER EMAIL="William.Cooke@noaa.gov"> William Cooke
+! </REVIEWER>
+!
+! <OVERVIEW>
+!  This module drives the generic version of tracers TOPAZ and CFC
+! </OVERVIEW>
+!----------------------------------------------------------------
+
 end module MOM_generic_tracer

From 46110923c0412f5d51f983dfcf76755f1fc8560d Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Fri, 29 Sep 2017 09:30:32 -0800
Subject: [PATCH 7/8] Modifying Area_h for OBCs.

---
 src/core/MOM_CoriolisAdv.F90 | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/src/core/MOM_CoriolisAdv.F90 b/src/core/MOM_CoriolisAdv.F90
index fd015b3262..c32352acb1 100644
--- a/src/core/MOM_CoriolisAdv.F90
+++ b/src/core/MOM_CoriolisAdv.F90
@@ -224,6 +224,27 @@ subroutine CorAdCalc(u, v, h, uh, vh, CAu, CAv, OBC, AD, G, GV, CS)
   do j=Jsq-1,Jeq+2 ; do I=Isq-1,Ieq+2
     Area_h(i,j) = G%mask2dT(i,j) * G%areaT(i,j)
   enddo ; enddo
+  if (associated(OBC)) then ; do n=1,OBC%number_of_segments
+    if (.not. OBC%segment(n)%on_pe) cycle
+    I = OBC%segment(n)%HI%IsdB ; J = OBC%segment(n)%HI%JsdB
+    if (OBC%segment(n)%is_N_or_S .and. (J >= Jsq-1) .and. (J <= Jeq+1)) then
+      do i = max(Isq-1,OBC%segment(n)%HI%isd), min(Ieq+2,OBC%segment(n)%HI%ied)
+        if (OBC%segment(n)%direction == OBC_DIRECTION_N) then
+          Area_h(i,j+1) = Area_h(i,j)
+        else ! (OBC%segment(n)%direction == OBC_DIRECTION_S)
+          Area_h(i,j) = Area_h(i,j+1)
+        endif
+      enddo
+    elseif (OBC%segment(n)%is_E_or_W .and. (I >= Isq-1) .and. (I <= Ieq+1)) then
+      do j = max(Jsq-1,OBC%segment(n)%HI%jsd), min(Jeq+2,OBC%segment(n)%HI%jed)
+        if (OBC%segment(n)%direction == OBC_DIRECTION_E) then
+          Area_h(i+1,j) = Area_h(i,j)
+        else ! (OBC%segment(n)%direction == OBC_DIRECTION_W)
+          Area_h(i,j) = Area_h(i+1,j)
+        endif
+      enddo
+    endif
+  enddo ; endif
   !$OMP parallel do default(private) shared(Isq,Ieq,Jsq,Jeq,G,Area_h,Area_q)
   do J=Jsq-1,Jeq+1 ; do I=Isq-1,Ieq+1
     Area_q(i,j) = (Area_h(i,j) + Area_h(i+1,j+1)) + &

From 72a2d517977ddd48d72f2026ff16b3effeefd0aa Mon Sep 17 00:00:00 2001
From: Kate Hedstrom <kshedstrom@alaska.edu>
Date: Mon, 2 Oct 2017 13:00:56 -0800
Subject: [PATCH 8/8] Clean out MOM6-examples in travis

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index f211d9f162..28fcdc6178 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -22,6 +22,7 @@ cache:
 # Install tools and clone the configurations repository
 before_install:
  - git clone https://github.com/adcroft/house_cleaning.git
+ - rm -rf MOM6-examples/
  # This line clones MOM6-examples when there is no cache
  - test -f MOM6-examples/README.md || (rm -rf MOM6-examples && git clone https://github.com/NOAA-GFDL/MOM6-examples.git)