Fix 6 low-risk pre-process bugs (batch) (#1241)

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

Author: sbryngelson

src/common/m_constants.fpp

@@ -44,7 +44,7 @@ module m_constants
     ! Interface Compression
     real(wp), parameter :: dflt_ic_eps = 1e-4_wp !< Ensure compression is only applied to surface cells in THINC
     real(wp), parameter :: dflt_ic_beta = 1.6_wp !< Sharpness parameter's default value used in THINC
-    integer, parameter :: moncon_cutoff = 1e-8_wp !< Monotonicity constraint's limiter to prevent extremas in THINC
+    real(wp), parameter :: moncon_cutoff = 1e-8_wp !< Monotonicity constraint's limiter to prevent extremas in THINC
 
     ! Chemistry
     real(wp), parameter :: dflt_T_guess = 1200._wp ! Default guess for temperature (when a previous value is not available)

src/pre_process/m_assign_variables.fpp

@@ -38,9 +38,9 @@ module m_assign_variables
         !> Skeleton of s_assign_patch_mixture_primitive_variables
         !!      and s_assign_patch_species_primitive_variables
         !! @param patch_id is the patch identifier
-        !! @param j (x) cell index in which the mixture or species primitive variables from the indicated patch areassigned
-        !! @param k (y,th) cell index in which the mixture or species primitive variables from the indicated patch areassigned
-        !! @param l (z) cell index in which the mixture or species primitive variables from the indicated patch areassigned
+        !! @param j (x) cell index in which the mixture or species primitive variables from the indicated patch are assigned
+        !! @param k (y,th) cell index in which the mixture or species primitive variables from the indicated patch are assigned
+        !! @param l (z) cell index in which the mixture or species primitive variables from the indicated patch are assigned
         !! @param eta pseudo volume fraction
         !! @param q_prim_vf Primitive variables
         !! @param patch_id_fp Array to track patch ids
@@ -233,7 +233,6 @@ contains
         if (qbmm) then
             do i = 1, nb
                 R3bar = R3bar + weight(i)*0.5_wp*(q_prim_vf(bubxb + 1 + (i - 1)*nmom)%sf(j, k, l))**3._wp
-                R3bar = R3bar + weight(i)*0.5_wp*(q_prim_vf(bubxb + 1 + (i - 1)*nmom)%sf(j, k, l))**3._wp
             end do
         else
             do i = 1, nb

src/pre_process/m_grid.f90

@@ -131,7 +131,7 @@ impure subroutine s_generate_serial_grid
             end do
 
             y_cb = y_cb*length
-            y_cc(0:m) = (y_cb(0:n) + y_cb(-1:n - 1))/2._wp
+            y_cc(0:n) = (y_cb(0:n) + y_cb(-1:n - 1))/2._wp
 
             dy = minval(y_cb(0:n) - y_cb(-1:n - 1))
 
@@ -168,7 +168,7 @@ impure subroutine s_generate_serial_grid
             end do
 
             z_cb = z_cb*length
-            z_cc(0:m) = (z_cb(0:p) + z_cb(-1:p - 1))/2._wp
+            z_cc(0:p) = (z_cb(0:p) + z_cb(-1:p - 1))/2._wp
 
             dz = minval(z_cb(0:p) - z_cb(-1:p - 1))
 

src/pre_process/m_mpi_proxy.fpp

@@ -76,10 +76,6 @@ contains
                 call MPI_BCAST(patch_bc(i)%${VAR}$, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
             #:endfor
 
-            #:for VAR in ['vel', 'angular_vel', 'angles']
-                call MPI_BCAST(patch_ib(i)%${VAR}$, 3, mpi_p, 0, MPI_COMM_WORLD, ierr)
-            #:endfor
-
             call MPI_BCAST(patch_bc(i)%radius, 1, mpi_p, 0, MPI_COMM_WORLD, ierr)
 
             #:for VAR in ['centroid', 'length']
@@ -120,7 +116,11 @@ contains
             if (chemistry) then
                 call MPI_BCAST(patch_icpp(i)%Y, size(patch_icpp(i)%Y), mpi_p, 0, MPI_COMM_WORLD, ierr)
             end if
-            ! Broadcast IB variables
+            ! Broadcast IB variables: patch_ib is indexed 1:num_patches_max,
+            ! not 1:num_bc_patches_max, so these must live in the num_patches_max loop.
+            #:for VAR in ['vel', 'angular_vel', 'angles']
+                call MPI_BCAST(patch_ib(i)%${VAR}$, size(patch_ib(i)%${VAR}$), mpi_p, 0, MPI_COMM_WORLD, ierr)
+            #:endfor
             call MPI_BCAST(patch_ib(i)%geometry, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
             call MPI_BCAST(patch_ib(i)%model_filepath, len(patch_ib(i)%model_filepath), MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr)
             call MPI_BCAST(patch_ib(i)%model_threshold, 1, mpi_p, 0, MPI_COMM_WORLD, ierr)

src/pre_process/m_perturbation.fpp

@@ -83,8 +83,8 @@ contains
                     perturb_alpha = q_prim_vf(E_idx + perturb_flow_fluid)%sf(i, j, k)
                     call random_number(rand_real)
                     rand_real = rand_real*perturb_flow_mag
-                    q_prim_vf(mom_idx%beg)%sf(i, j, k) = (1._wp + rand_real)*q_prim_vf(mom_idx%beg)%sf(i, j, k)
                     q_prim_vf(mom_idx%end)%sf(i, j, k) = rand_real*q_prim_vf(mom_idx%beg)%sf(i, j, k)
+                    q_prim_vf(mom_idx%beg)%sf(i, j, k) = (1._wp + rand_real)*q_prim_vf(mom_idx%beg)%sf(i, j, k)
                     if (bubbles_euler) then
                         q_prim_vf(alf_idx)%sf(i, j, k) = (1._wp + rand_real)*q_prim_vf(alf_idx)%sf(i, j, k)
                     end if
@@ -245,7 +245,7 @@ contains
 
     !>  This subroutine computes velocity perturbations for a temporal mixing
         !!              layer with a hyperbolic tangent mean streamwise velocity
-        !!              profile, using an inverter version of the spectrum-based
+        !!              profile, using an inverted version of the spectrum-based
         !!              synthetic turbulence generation method proposed by
         !!              Guo et al. (2023, JFM).
     subroutine s_perturb_mixlayer(q_prim_vf)

src/pre_process/m_start_up.fpp

@@ -2,6 +2,8 @@
 !! @file
 !! @brief Contains module m_start_up
 
+#:include 'macros.fpp'
+
 !> @brief Reads and validates user inputs, loads existing grid/IC data, and initializes pre-process modules
 module m_start_up
 
@@ -767,7 +769,8 @@ contains
 
         real(wp), intent(inout) :: start, finish
 
-        integer :: j, k
+        integer :: j, k, l
+        real(wp) :: r2
 
         ! Setting up the grid and the initial condition. If the grid is read in from
         ! preexisting grid data files, it is checked for consistency. If the grid is
@@ -787,10 +790,16 @@ contains
 
         ! hard-coded psi
         if (hyper_cleaning) then
-            do j = 0, m
+            @:ASSERT(psi_idx > 0, "hyper_cleaning requires psi_idx to be set")
+            do l = 0, p
                 do k = 0, n
-                    q_cons_vf(psi_idx)%sf(j, k, 0) = 1d-2*exp(-(x_cc(j)**2 + y_cc(k)**2)/(2.0*0.05**2))
-                    q_prim_vf(psi_idx)%sf(j, k, 0) = q_cons_vf(psi_idx)%sf(j, k, 0)
+                    do j = 0, m
+                        r2 = x_cc(j)**2
+                        if (n > 0) r2 = r2 + y_cc(k)**2
+                        if (p > 0) r2 = r2 + z_cc(l)**2
+                        q_cons_vf(psi_idx)%sf(j, k, l) = 1.0e-2_wp*exp(-r2/(2.0_wp*0.05_wp**2))
+                        q_prim_vf(psi_idx)%sf(j, k, l) = q_cons_vf(psi_idx)%sf(j, k, l)
+                    end do
                 end do
             end do
         end if