Rename component `list_vis` of snapshot to list

Rename component `list_vis` of derived type snapshot to list. Since
there are no longer invisible (interpolated) eddies.

Common/derived_types.f90

@@ -39,10 +39,10 @@ module derived_types
   end type eddy
 
   type snapshot
-     type(eddy), allocatable:: list_vis(:) ! (number_extr)
+     type(eddy), allocatable:: list(:) ! (number_extr)
      ! Visible "eddies" at a given date. These include "eddies"
      ! without an outermost contour, that is only the extremum is
-     ! visible. The subscript value in list_vis is the "identification
+     ! visible. The subscript value in list is the "identification
      ! number" of the extremum.
      
      integer number_extr ! number of visible extrema

Common/read_snapshot.f90

@@ -49,7 +49,7 @@ contains
     end if
 
     s%number_extr = ishape_last(k + 1) - ishape_first + 1
-    allocate(s%list_vis(s%number_extr))
+    allocate(s%list(s%number_extr))
 
     do ishape = ishape_first, ishape_last(k + 1)
        call read_eddy(e, d, i, hshp, ishape)
@@ -57,12 +57,12 @@ contains
        ! Check that all the eddies have the same date index:
        call assert(d - d_init == k, "read_snapshot: date index")
 
-       s%list_vis(i) = e
+       s%list(i) = e
     end do
 
     allocate(s%ind_extr(2, s%number_extr))
     forall (i = 1:s%number_extr) s%ind_extr(:, i) &
-         = nint(convert_to_ind(s%list_vis(i)%coord_extr, corner, step))
+         = nint(convert_to_ind(s%list(i)%coord_extr, corner, step))
 
     ! Define s%extr_map from s%ind_extr:
 

Inst_eddies/Tests/test_nearby_extr.f90

@@ -55,7 +55,7 @@ program test_nearby_extr
        copy = 0, ishape_last = [ishape_last])
   CALL shpc_close(hshp)
 
-  nearby = nearby_extr(s%extr_map, s%list_vis, i = 4)
+  nearby = nearby_extr(s%extr_map, s%list, i = 4)
   print *, "nearby:"
 
   do l = 1, size(nearby, 2)

Inst_eddies/Tests/test_set_all_outerm.f90

@@ -83,9 +83,9 @@ program test_set_all_outerm
        min_area = pi * (min_radius * 1e3)**2)
 
   do i = 1, s%number_extr
-     s%list_vis(i)%speed_cont = null_ssh_contour()
-     s%list_vis(i)%max_speed = missing_speed
-     s%list_vis(i)%radius4 = 0
+     s%list(i)%speed_cont = null_ssh_contour()
+     s%list(i)%max_speed = missing_speed
+     s%list(i)%radius4 = 0
   end do
 
   call shpc_create(hshp_cyclo, shpc_dir = "SHPC_cyclo", cyclone = .true.)
@@ -94,12 +94,12 @@ program test_set_all_outerm
   n_anti = 0
 
   do i = 1, s%number_extr
-     if (s%list_vis(i)%cyclone) then
+     if (s%list(i)%cyclone) then
         n_cyclo = n_cyclo + 1
-        call write_eddy(s%list_vis(i), hshp_cyclo, days_1950 = 1, i = n_cyclo)
+        call write_eddy(s%list(i), hshp_cyclo, days_1950 = 1, i = n_cyclo)
      else
         n_anti = n_anti + 1
-        call write_eddy(s%list_vis(i), hshp_anti, days_1950 = 1, i = n_anti)
+        call write_eddy(s%list(i), hshp_anti, days_1950 = 1, i = n_anti)
      end if
   end do
 
@@ -109,6 +109,6 @@ program test_set_all_outerm
   CALL shpc_close(hshp_anti)
   print *, 'Created shapefile collections in SHPC_cyclo and SHPC_anti.'
   print *, "Average number of points per outermost contour: ", &
-       sum(s%list_vis%out_cont%n_points) / real(s%number_extr)
+       sum(s%list%out_cont%n_points) / real(s%number_extr)
 
 end program test_set_all_outerm

Inst_eddies/inst_eddies.f90

@@ -143,14 +143,14 @@ program inst_eddies
   ! max-speed contours.
 
   do i = 1, s%number_extr
-     if (s%list_vis(i)%valid) then
+     if (s%list(i)%valid) then
         ! Restrict the field to the outermost contour:
 
-        llc = floor(convert_to_ind(minval(s%list_vis(i)%out_cont%points, &
+        llc = floor(convert_to_ind(minval(s%list(i)%out_cont%points, &
              dim = 2), corner, step))
 
         urc = ceiling(convert_to_ind(maxval( &
-             s%list_vis(i)%out_cont%points, dim = 2), corner, step))
+             s%list(i)%out_cont%points, dim = 2), corner, step))
 
         ! Should have no effect except because of roundup error:
         urc(2) = min(urc(2), nlat)
@@ -159,7 +159,7 @@ program inst_eddies
         corner_window = corner + (llc - 1) * step
 
         outside_points = nearby_extr(s%extr_map(llc(1):urc(1), &
-             llc(2):urc(2)), s%list_vis, i)
+             llc(2):urc(2)), s%list, i)
 
         if (periodic) outside_points(1, :) = outside_points(1, :) &
              + ceiling((corner_window(1) - outside_points(1, :)) / twopi) &
@@ -167,14 +167,14 @@ program inst_eddies
         ! (Shift the longitude of each point to a value close to
         ! the longitude of the target extremum.)
 
-        call set_max_speed(s%list_vis(i), s%ind_extr(:, i) - llc + 1, &
+        call set_max_speed(s%list(i), s%ind_extr(:, i) - llc + 1, &
              outside_points, ssh(llc(1):urc(1), llc(2):urc(2)), &
              u(llc(1):urc(1), llc(2):urc(2)), &
              v(llc(1):urc(1), llc(2):urc(2)), corner_window, step)
      else
-        s%list_vis(i)%speed_cont = null_ssh_contour()
-        s%list_vis(i)%max_speed = missing_speed
-        s%list_vis(i)%radius4 = 0
+        s%list(i)%speed_cont = null_ssh_contour()
+        s%list(i)%max_speed = missing_speed
+        s%list(i)%radius4 = 0
      end if
   end do
 
@@ -194,12 +194,12 @@ program inst_eddies
   n_anti = 0
 
   do i = 1, s%number_extr
-     if (s%list_vis(i)%cyclone) then
+     if (s%list(i)%cyclone) then
         n_cyclo = n_cyclo + 1
-        call write_eddy(s%list_vis(i), hshpc_cyclo, days_1950, n_cyclo)
+        call write_eddy(s%list(i), hshpc_cyclo, days_1950, n_cyclo)
      else
         n_anti = n_anti + 1
-        call write_eddy(s%list_vis(i), hshpc_anti, days_1950, n_anti)
+        call write_eddy(s%list(i), hshpc_anti, days_1950, n_anti)
      end if
   end do
 

Inst_eddies/set_all_outerm.f90

@@ -24,7 +24,7 @@ contains
 
     type(snapshot), intent(out):: s
     ! Specifically: define everything in s except
-    ! s%list_vis%speed_cont, s%list_vis%max_speed and s%list_vis%radius4.
+    ! s%list%speed_cont, s%list%max_speed and s%list%radius4.
 
     integer, intent(in):: max_radius(:) ! (2) maximum radius of an
     ! eddy in longitude and latitude, in number of grid points
@@ -100,17 +100,17 @@ contains
     end if
 
     s%number_extr = size(s%ind_extr, 2)
-    allocate(s%list_vis(s%number_extr), sorted_extr(s%number_extr))
+    allocate(s%list(s%number_extr), sorted_extr(s%number_extr))
 
     forall (i = 1:s%number_extr)
-       s%list_vis(i)%coord_extr = corner + (s%ind_extr(:, i) - 1) * step
+       s%list(i)%coord_extr = corner + (s%ind_extr(:, i) - 1) * step
        ! (Even when periodic, this is within the original NetCDF grid,
        ! that is the grid without duplicated longitudes.)
        
-       s%list_vis(i)%ssh_extr = ssh(s%ind_extr(1, i), s%ind_extr(2, i))
-       s%list_vis(i)%cyclone = cyclone(i)
+       s%list(i)%ssh_extr = ssh(s%ind_extr(1, i), s%ind_extr(2, i))
+       s%list(i)%cyclone = cyclone(i)
 
-       s%list_vis(i)%valid = .true.
+       s%list(i)%valid = .true.
        ! must be intialized to true because it is used in nearby_extr
     end forall
 
@@ -118,11 +118,11 @@ contains
 
     selection = argwhere(cyclone)
     n_cycl = size(selection)
-    selection = selection(indexx(s%list_vis(selection)%ssh_extr))
+    selection = selection(indexx(s%list(selection)%ssh_extr))
     sorted_extr(:n_cycl) = selection(n_cycl:1:- 1) ! descending order of ssh
 
     selection = argwhere(.not. cyclone)
-    selection = selection(indexx(s%list_vis(selection)%ssh_extr))
+    selection = selection(indexx(s%list(selection)%ssh_extr))
     sorted_extr(n_cycl + 1:) = selection
 
     do l = 1, s%number_extr
@@ -144,20 +144,20 @@ contains
        corner_window = corner + (llc - 1) * step
 
        ! No need to consider contours with amplitudes < min_amp:
-       if (abs(s%list_vis(i)%ssh_extr - innermost_level(i)) < min_amp) &
-            innermost_level(i) = s%list_vis(i)%ssh_extr &
-            + merge(min_amp, - min_amp, s%list_vis(i)%cyclone)
+       if (abs(s%list(i)%ssh_extr - innermost_level(i)) < min_amp) &
+            innermost_level(i) = s%list(i)%ssh_extr &
+            + merge(min_amp, - min_amp, s%list(i)%cyclone)
        
        outside_points = nearby_extr(s%extr_map(llc(1):urc(1), llc(2):urc(2)), &
-            s%list_vis, i)
+            s%list, i)
        if (periodic) outside_points(1, :) = outside_points(1, :) &
             + ceiling((corner_window(1) - outside_points(1, :)) / twopi) * twopi
        ! (Shift the longitude of each point to a value close to the
        ! longitude of the target extremum.)
-       s%list_vis(i)%out_cont = get_1_outerm(s%list_vis(i)%cyclone, &
-            s%list_vis(i)%coord_extr, innermost_level(i), outside_points, &
+       s%list(i)%out_cont = get_1_outerm(s%list(i)%cyclone, &
+            s%list(i)%coord_extr, innermost_level(i), outside_points, &
             ssh(llc(1):urc(1), llc(2):urc(2)), corner_window, step)
-       s%list_vis(i)%valid = s%list_vis(i)%out_cont%area >= min_area
+       s%list(i)%valid = s%list(i)%out_cont%area >= min_area
     end do
 
   end subroutine set_all_outerm

Overlap/Tests/test_overlap.f90

@@ -83,12 +83,12 @@ program test_overlap
   call read_snapshot(flow(max_delta + 1), hshp, nlon, nlat, d_init, k_test_2, &
        corner, step, copy, ishape_last)
   CALL shpc_close(hshp)
-  print *, "Enter flow(1)%list_vis%delta_out (array with ", &
+  print *, "Enter flow(1)%list%delta_out (array with ", &
        flow(1)%number_extr, " values):"
-  read *, flow(1)%list_vis%delta_out
-  print *, "Enter flow(max_delta + 1)%list_vis%delta_in (array with ", &
+  read *, flow(1)%list%delta_out
+  print *, "Enter flow(max_delta + 1)%list%delta_in (array with ", &
        flow(max_delta + 1)%number_extr, " values)):"
-  read *, flow(max_delta + 1)%list_vis%delta_in
+  read *, flow(max_delta + 1)%list%delta_in
   call open_edge_file(rank = 0)
   call overlap(flow, nlon, nlat, periodic, dist_lim, e_overestim, &
        k = k_test_2, delta = max_delta, j = max_delta + 1)
@@ -98,7 +98,7 @@ program test_overlap
   print *, k_test_1, ":"
   print *, "Valid isolated eddies:"
   do i = 1, flow(1)%number_extr
-     if (flow(1)%list_vis(i)%valid .and. flow(1)%list_vis(i)%delta_out &
+     if (flow(1)%list(i)%valid .and. flow(1)%list(i)%delta_out &
           == huge(0)) write(unit = *, fmt = "(i0, 1x)", advance = "no") i
   end do
   print *
@@ -108,8 +108,8 @@ program test_overlap
   print *, "Valid isolated eddies:"
 
   do i = 1, flow(max_delta + 1)%number_extr
-     if (flow(max_delta + 1)%list_vis(i)%valid &
-          .and. flow(max_delta + 1)%list_vis(i)%delta_in == huge(0)) &
+     if (flow(max_delta + 1)%list(i)%valid &
+          .and. flow(max_delta + 1)%list(i)%delta_in == huge(0)) &
           write(unit = *, fmt = "(i0, 1x)", advance = "no") i
   end do
 

Overlap/Tests/write_snapshot.f90

@@ -35,11 +35,11 @@ contains
 
     !-----------------------------------------------------------------
 
-    call shpc_create(hshp, shpc_dir = "SHPC", cyclone = s%list_vis(1)%cyclone)
+    call shpc_create(hshp, shpc_dir = "SHPC", cyclone = s%list(1)%cyclone)
 
     ! Write snapshot:
     do i = 1, s%number_extr
-       call write_eddy(s%list_vis(i), hshp, d, i)
+       call write_eddy(s%list(i), hshp, d, i)
     end do
 
     CALL shpc_close(hshp)

Overlap/dispatch_snapshot.f90

@@ -27,8 +27,8 @@ contains
        d = k + d_init
        
        do i = 1, s%number_extr
-          if (s%list_vis(i)%valid .and. s%list_vis(i)%delta_in == huge(0) &
-               .and. s%list_vis(i)%delta_out == huge(0)) &
+          if (s%list(i)%valid .and. s%list(i)%delta_in == huge(0) &
+               .and. s%list(i)%delta_out == huge(0)) &
                write(unit_isolated, fmt = *) d, i
        end do
     else

Overlap/overlap.f90

@@ -9,8 +9,8 @@ contains
 
     ! This procedure finds edges between flow(j - delta) and flow(j),
     ! corresponding to date indices k - delta and k. It writes these
-    ! edges. It updates flow(j - delta)%list_vis%delta_out and
-    ! flow(j)%list_vis%delta_in.
+    ! edges. It updates flow(j - delta)%list%delta_out and
+    ! flow(j)%list%delta_in.
 
     ! Libraries:
     use contour_531, only: polyline
@@ -59,7 +59,7 @@ contains
     !-----------------------------------------------------------------------
 
     loop_i1: do i1 = 1, flow(j - delta)%number_extr
-       test_valid: if (flow(j - delta)%list_vis(i1)%valid) then
+       test_valid: if (flow(j - delta)%list(i1)%valid) then
           ! Define the geographical window around each eddy extremum:
 
           llc = flow(j - delta)%ind_extr(:, i1) - dist_lim
@@ -75,35 +75,35 @@ contains
 
           ! Pre-select potential successors:
           selection = candidate_overlap(flow(j)%extr_map(llc(1):urc(1), &
-               llc(2):urc(2)), flow(j)%list_vis, &
-               flow(j - delta)%list_vis(i1)%delta_out, delta)
+               llc(2):urc(2)), flow(j)%list, &
+               flow(j - delta)%list(i1)%delta_out, delta)
           
           n_select = size(selection)
 
           if (n_select /= 0) then
-             if (flow(j - delta)%list_vis(i1)%speed_cont%n_points /= 0) then
-                polyline_1 = flow(j - delta)%list_vis(i1)%speed_cont%polyline
+             if (flow(j - delta)%list(i1)%speed_cont%n_points /= 0) then
+                polyline_1 = flow(j - delta)%list(i1)%speed_cont%polyline
              else
-                polyline_1 = flow(j - delta)%list_vis(i1)%out_cont%polyline
+                polyline_1 = flow(j - delta)%list(i1)%out_cont%polyline
              end if
           end if
 
           DO l = 1, n_select
              i2 = selection(l)
-             ! Assertion: {flow(j - delta)%list_vis(i1)%delta_out >=
-             ! delta .or. flow(j)%list_vis(i2)%delta_in >= delta}
+             ! Assertion: {flow(j - delta)%list(i1)%delta_out >=
+             ! delta .or. flow(j)%list(i2)%delta_in >= delta}
 
-             if (flow(j)%list_vis(i2)%speed_cont%n_points /= 0) then
-                polyline_2 = flow(j)%list_vis(i2)%speed_cont%polyline
+             if (flow(j)%list(i2)%speed_cont%n_points /= 0) then
+                polyline_2 = flow(j)%list(i2)%speed_cont%polyline
              else
-                polyline_2 = flow(j)%list_vis(i2)%out_cont%polyline
+                polyline_2 = flow(j)%list(i2)%out_cont%polyline
              end if
 
              ! Shift the longitudes of polyline_2 to values close to the
              ! longitude of extremum i1:
              polyline_2%points(1, :) = polyline_2%points(1, :) &
-                  + floor((flow(j - delta)%list_vis(i1)%coord_extr(1) &
-                  - flow(j)%list_vis(i2)%coord_extr(1)) / twopi + 0.5) * twopi
+                  + floor((flow(j - delta)%list(i1)%coord_extr(1) &
+                  - flow(j)%list(i2)%coord_extr(1)) / twopi + 0.5) * twopi
 
              call gpc_polygon_clip_f(GPC_INT, &
                   polygon(nparts = 1, part = [polyline_1], hole = [.false.]), &
@@ -117,12 +117,12 @@ contains
                      spher_polyline_area(polyline_2))) then
                    write(unit_edge, fmt = *) (k - delta) * e_overestim + i1, &
                         k * e_overestim + i2, &
-                        weight(flow(j - delta)%list_vis(i1), &
-                        flow(j)%list_vis(i2))
-                   flow(j - delta)%list_vis(i1)%delta_out &
-                        = min(flow(j - delta)%list_vis(i1)%delta_out, delta)
-                   flow(j)%list_vis(i2)%delta_in &
-                        = min(flow(j)%list_vis(i2)%delta_in, delta)
+                        weight(flow(j - delta)%list(i1), &
+                        flow(j)%list(i2))
+                   flow(j - delta)%list(i1)%delta_out &
+                        = min(flow(j - delta)%list(i1)%delta_out, delta)
+                   flow(j)%list(i2)%delta_in &
+                        = min(flow(j)%list(i2)%delta_in, delta)
                 end if
              end if
           end DO

Overlap/recv_snapshot.f90

@@ -27,19 +27,19 @@ contains
     !-----------------------------------------------------------
 
     call ezmpi_recv(s%number_extr, source, tag)
-    allocate(s%list_vis(s%number_extr))
+    allocate(s%list(s%number_extr))
 
     do i = 1, s%number_extr
-       call ezmpi_recv(s%list_vis(i)%coord_extr, source, tag)
-       call ezmpi_recv(s%list_vis(i)%ssh_extr, source, tag)
-       call ezmpi_recv(s%list_vis(i)%cyclone, source, tag)
-       call recv_ssh_contour(s%list_vis(i)%out_cont, source, tag)
-       call recv_ssh_contour(s%list_vis(i)%speed_cont, source, tag)
-       call ezmpi_recv(s%list_vis(i)%max_speed, source, tag)
-       call ezmpi_recv(s%list_vis(i)%valid, source, tag)
-       call ezmpi_recv(s%list_vis(i)%delta_in, source, tag)
-       call ezmpi_recv(s%list_vis(i)%delta_out, source, tag)
-       call ezmpi_recv(s%list_vis(i)%radius4, source, tag)
+       call ezmpi_recv(s%list(i)%coord_extr, source, tag)
+       call ezmpi_recv(s%list(i)%ssh_extr, source, tag)
+       call ezmpi_recv(s%list(i)%cyclone, source, tag)
+       call recv_ssh_contour(s%list(i)%out_cont, source, tag)
+       call recv_ssh_contour(s%list(i)%speed_cont, source, tag)
+       call ezmpi_recv(s%list(i)%max_speed, source, tag)
+       call ezmpi_recv(s%list(i)%valid, source, tag)
+       call ezmpi_recv(s%list(i)%delta_in, source, tag)
+       call ezmpi_recv(s%list(i)%delta_out, source, tag)
+       call ezmpi_recv(s%list(i)%radius4, source, tag)
     end do
 
     allocate(s%extr_map(1 - copy:nlon + copy, nlat))

Overlap/send_snapshot.f90

@@ -25,16 +25,16 @@ contains
     call ezmpi_send(s%number_extr, dest, tag)
 
     do i = 1, s%number_extr
-       call ezmpi_send(s%list_vis(i)%coord_extr, dest, tag)
-       call ezmpi_send(s%list_vis(i)%ssh_extr, dest, tag)
-       call ezmpi_send(s%list_vis(i)%cyclone, dest, tag)
-       call send_ssh_contour(s%list_vis(i)%out_cont, dest, tag)
-       call send_ssh_contour(s%list_vis(i)%speed_cont, dest, tag)
-       call ezmpi_send(s%list_vis(i)%max_speed, dest, tag)
-       call ezmpi_send(s%list_vis(i)%valid, dest, tag)
-       call ezmpi_send(s%list_vis(i)%delta_in, dest, tag)
-       call ezmpi_send(s%list_vis(i)%delta_out, dest, tag)
-       call ezmpi_send(s%list_vis(i)%radius4, dest, tag)
+       call ezmpi_send(s%list(i)%coord_extr, dest, tag)
+       call ezmpi_send(s%list(i)%ssh_extr, dest, tag)
+       call ezmpi_send(s%list(i)%cyclone, dest, tag)
+       call send_ssh_contour(s%list(i)%out_cont, dest, tag)
+       call send_ssh_contour(s%list(i)%speed_cont, dest, tag)
+       call ezmpi_send(s%list(i)%max_speed, dest, tag)
+       call ezmpi_send(s%list(i)%valid, dest, tag)
+       call ezmpi_send(s%list(i)%delta_in, dest, tag)
+       call ezmpi_send(s%list(i)%delta_out, dest, tag)
+       call ezmpi_send(s%list(i)%radius4, dest, tag)
     end do
 
     call ezmpi_send(s%extr_map, dest, tag)