Fix 6 safe pre/post-process bugs (batch) (#1240)

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson

src/common/m_model.fpp

@@ -241,14 +241,14 @@ contains
     end subroutine s_read_stl
 
     !> This procedure reads an OBJ file.
-    !! @param filepath Path to the odj file.
+    !! @param filepath Path to the obj file.
     !! @param model The obj file.
     impure subroutine s_read_obj(filepath, model)
 
         character(LEN=*), intent(in) :: filepath
         type(t_model), intent(out) :: model
 
-        integer :: i, j, k, l, iunit, iostat, nVertices
+        integer :: i, j, k, l, iv3, iunit, iostat, nVertices
 
         real(wp), dimension(1:3), allocatable :: vertices(:, :)
 
@@ -297,10 +297,10 @@ contains
                 read (line(3:), *) vertices(i, :)
                 i = i + 1
             case ("f ")
-                read (line(3:), *) k, l, j
+                read (line(3:), *) k, l, iv3
                 model%trs(j)%v(1, :) = vertices(k, :)
                 model%trs(j)%v(2, :) = vertices(l, :)
-                model%trs(j)%v(3, :) = vertices(j, :)
+                model%trs(j)%v(3, :) = vertices(iv3, :)
                 j = j + 1
             case default
                 print *, "Error: unknown line type in OBJ file ", filepath

src/post_process/m_data_output.fpp

@@ -1102,6 +1102,7 @@ contains
         call MPI_BCAST(file_time, 1, mpi_p, 0, MPI_COMM_WORLD, ierr)
         call MPI_BCAST(file_dt, 1, mpi_p, 0, MPI_COMM_WORLD, ierr)
         call MPI_BCAST(file_num_procs, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
+        time_real = file_time
 
         allocate (proc_bubble_counts(file_num_procs))
 
@@ -1271,6 +1272,7 @@ contains
         call MPI_BCAST(file_time, 1, mpi_p, 0, MPI_COMM_WORLD, ierr)
         call MPI_BCAST(file_dt, 1, mpi_p, 0, MPI_COMM_WORLD, ierr)
         call MPI_BCAST(file_num_procs, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
+        time_real = file_time
 
         allocate (proc_bubble_counts(file_num_procs))
 
@@ -1546,19 +1548,16 @@ contains
                         counter = counter + 1
                         x_d1(counter) = x_cc(j)
                         y_d1(counter) = y_cc(k)
-                        euc_d = sqrt((x_cc(j) - x_d1(i))**2 + (y_cc(k) - y_d1(i))**2)
-                        tgp = sqrt(dx(j)**2 + dy(k)**2)
                     else
-                        euc_d = sqrt((x_cc(j) - x_d1(i))**2 + (y_cc(k) - y_d1(i))**2)
                         tgp = sqrt(dx(j)**2 + dy(k)**2)
                         do i = 1, counter
+                            euc_d = sqrt((x_cc(j) - x_d1(i))**2 + (y_cc(k) - y_d1(i))**2)
                             if (euc_d < tgp) then
-                                cycle
-                            elseif (euc_d > tgp .and. i == counter) then
+                                exit
+                            elseif (i == counter) then
                                 counter = counter + 1
                                 x_d1(counter) = x_cc(j)
                                 y_d1(counter) = y_cc(k)
-
                             end if
                         end do
                     end if

src/pre_process/m_simplex_noise.fpp

@@ -205,8 +205,8 @@ contains
         x2 = x0 - 1._wp + 2._wp*G2
         y2 = y0 - 1._wp + 2._wp*G2
 
-        ii = mod(i, 255)
-        jj = mod(j, 255)
+        ii = iand(i, 255)
+        jj = iand(j, 255)
 
         gi0 = mod(p_vec(ii + p_vec(jj)), 10) + 1
         gi1 = mod(p_vec(ii + i1 + p_vec(jj + j1)), 10) + 1

src/pre_process/m_start_up.fpp

@@ -357,7 +357,7 @@ contains
         ! the time-step directory that will contain the new grid and initial
         ! condition data are also generated.
         if (old_ic .neqv. .true.) then
-            call s_delete_directory(trim(proc_rank_dir)//'/*')
+            call s_delete_directory(trim(proc_rank_dir))
             call s_create_directory(trim(proc_rank_dir)//'/0')
         end if
 
@@ -507,7 +507,7 @@ contains
         ! process may be cleaned out to make room for new pre-process data.
         ! In addition, the time-step folder that will contain the new grid
         ! and initial condition data are also generated.
-        call s_create_directory(trim(proc_rank_dir)//'/*')
+        call s_delete_directory(trim(proc_rank_dir))
         call s_create_directory(trim(proc_rank_dir)//'/0')
 
     end subroutine s_read_serial_ic_data_files

src/simulation/m_global_parameters.fpp

@@ -815,8 +815,8 @@ contains
             integral(i)%xmax = dflt_real
             integral(i)%ymin = dflt_real
             integral(i)%ymax = dflt_real
-            integral(i)%ymin = dflt_real
-            integral(i)%ymax = dflt_real
+            integral(i)%zmin = dflt_real
+            integral(i)%zmax = dflt_real
         end do
 
         ! GRCBC flags