From 89a0ac5517aea9498685250dc5c4705bcac6840e Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Fri, 12 Dec 2025 13:48:00 -0500
Subject: [PATCH 01/34] Added ellipse marker patch

---
 src/common/m_ib_patches.fpp | 44 +++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/src/common/m_ib_patches.fpp b/src/common/m_ib_patches.fpp
index c0d95e6f12..18fcf5968e 100644
--- a/src/common/m_ib_patches.fpp
+++ b/src/common/m_ib_patches.fpp
@@ -119,6 +119,9 @@ contains
                     ! STL+IBM patch
                 elseif (patch_ib(i)%geometry == 5) then
                     call s_ib_model(i, ib_markers_sf, levelset, levelset_norm)
+                elseif (patch_ib(i)%geometry == 6) then
+                    call s_ib_ellipse(i, ib_markers_sf)
+                    call s_ellipse_levelset(i, levelset, levelset_norm)
                 end if
             end do
             !> @}
@@ -762,6 +765,47 @@ contains
 
     end subroutine s_ib_cylinder
 
+
+    subroutine s_ib_ellipse(patch_id, ib_markers_sf)
+
+        integer, intent(in) :: patch_id
+        integer, dimension(0:m, 0:n, 0:p), intent(inout) :: ib_markers_sf
+
+        integer :: i, j, k !< generic loop iterators
+        real(wp), dimension(1:3) :: xy_local !< x and y coordinates in local IB frame
+        real(wp), dimension(1:2) :: length, center !< x and y coordinates in local IB frame
+        real(wp), dimension(1:3, 1:3) :: inverse_rotation
+
+        ! Transferring the rectangle's centroid and length information
+        center(1) = patch_ib(patch_id)%x_centroid
+        center(2) = patch_ib(patch_id)%y_centroid
+        length(1) = patch_ib(patch_id)%length_x
+        length(2) = patch_ib(patch_id)%length_y
+        inverse_rotation(:, :) = patch_ib(patch_id)%rotation_matrix_inverse(:, :)
+
+        ! Checking whether the rectangle covers a particular cell in the
+        ! domain and verifying whether the current patch has the permission
+        ! to write to that cell. If both queries check out, the primitive
+        ! variables of the current patch are assigned to this cell.
+        $:GPU_PARALLEL_LOOP(private='[i,j, xy_local]', copy='[ib_markers_sf]',&
+                  & copyin='[patch_id,center,length,inverse_rotation,x_cc,y_cc]', collapse=2)
+        do j = 0, n
+            do i = 0, m
+                ! get the x and y coordinates in the local IB frame
+                xy_local = [x_cc(i) - center(1), y_cc(j) - center(2), 0._wp]
+                xy_local = matmul(inverse_rotation, xy_local)
+
+                ! Ellipse condition (x/a)^2 + (y/b)^2 <= 1
+                if ((xy_local(1)/length(1))**2 + (xy_local(1)/length(1))**2) then
+                    ! Updating the patch identities bookkeeping variable
+                    ib_markers_sf(i, j, 0) = patch_id
+                end if
+            end do
+        end do
+        $:END_GPU_PARALLEL_LOOP()
+
+    end subroutine s_ib_ellipse
+
     !> The STL patch is a 2/3D geometry that is imported from an STL file.
     !! @param patch_id is the patch identifier
     !! @param ib_markers_sf Array to track patch ids

From ef446f5addc81da2c82c13ec236ab4da5464d222 Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Fri, 12 Dec 2025 16:40:40 -0500
Subject: [PATCH 02/34] Added ellipse IB patch

---
 src/common/m_compute_levelset.fpp      | 59 +++++++++++++++++++++++++-
 src/common/m_ib_patches.fpp            | 11 ++---
 src/pre_process/m_check_ib_patches.fpp |  2 +
 3 files changed, 66 insertions(+), 6 deletions(-)

diff --git a/src/common/m_compute_levelset.fpp b/src/common/m_compute_levelset.fpp
index f343c0c47c..5346eb1b8b 100644
--- a/src/common/m_compute_levelset.fpp
+++ b/src/common/m_compute_levelset.fpp
@@ -23,7 +23,8 @@ module m_compute_levelset
  s_3D_airfoil_levelset, &
  s_rectangle_levelset, &
  s_cuboid_levelset, &
- s_sphere_levelset
+ s_sphere_levelset, &
+ s_ellipse_levelset
 
 contains
 
@@ -336,6 +337,62 @@ contains
 
     end subroutine s_rectangle_levelset
 
+    subroutine s_ellipse_levelset(ib_patch_id, levelset, levelset_norm)
+
+        type(levelset_field), intent(INOUT), optional :: levelset
+        type(levelset_norm_field), intent(INOUT), optional :: levelset_norm
+
+        integer, intent(in) :: ib_patch_id
+        real(wp) :: ellipse_coeffs(2) ! a and b in the ellipse equation
+        real(wp) :: quadratic_coeffs(3) ! A, B, C in the quadratic equation to compute levelset
+
+        real(wp) :: length_x, length_y
+        real(wp), dimension(1:3) :: xy_local, normal_vector !< x and y coordinates in local IB frame
+        real(wp), dimension(2) :: center !< x and y coordinates in local IB frame
+        real(wp), dimension(1:3, 1:3) :: rotation, inverse_rotation
+
+        integer :: i, j, k !< Loop index variables
+        integer :: idx !< Shortest path direction indicator
+
+        length_x = patch_ib(ib_patch_id)%length_x
+        length_y = patch_ib(ib_patch_id)%length_y
+        center(1) = patch_ib(ib_patch_id)%x_centroid
+        center(2) = patch_ib(ib_patch_id)%y_centroid
+        inverse_rotation(:, :) = patch_ib(ib_patch_id)%rotation_matrix_inverse(:, :)
+        rotation(:, :) = patch_ib(ib_patch_id)%rotation_matrix(:, :)
+
+        ellipse_coeffs(1) = 0.5_wp * length_x
+        ellipse_coeffs(2) = 0.5_wp * length_y
+
+        $:GPU_PARALLEL_LOOP(private='[i,j,k,idx,quadratic_coeffs,xy_local,normal_vector]', &
+                  & copyin='[ib_patch_id,center,ellipse_coeffs,inverse_rotation,rotation]', collapse=2)
+        do i = 0, m
+            do j = 0, n
+                xy_local = [x_cc(i) - center(1), y_cc(j) - center(2), 0._wp]
+                xy_local = matmul(inverse_rotation, xy_local)
+
+                ! we will get NaNs in the levelset if we compute this outside the ellipse
+                if ((xy_local(1)/ellipse_coeffs(1))**2 + (xy_local(2)/ellipse_coeffs(2))**2 <= 1._wp) then
+
+                    normal_vector = xy_local
+                    normal_vector(2) = normal_vector(2) * (ellipse_coeffs(1)/ellipse_coeffs(2))**2._wp ! get the normal direction via the coordinate transofmration method
+                    normal_vector = normal_vector / sqrt(dot_product(normal_vector, normal_vector)) ! normalize the vector
+                    levelset_norm%sf(i, j, 0, ib_patch_id, :) = matmul(rotation, normal_vector) ! save after rotating the vector to the global frame
+
+                    ! use the normal vector to set up the quadratic equation for the levelset, using A, B, and C in indices 1, 2, and 3
+                    quadratic_coeffs(1) = (normal_vector(1)/ellipse_coeffs(1))**2 + (normal_vector(2)/ellipse_coeffs(2))**2
+                    quadratic_coeffs(2) = 2._wp * ((xy_local(1)*normal_vector(1)/(ellipse_coeffs(1)**2)) + (xy_local(2)*normal_vector(2)/(ellipse_coeffs(2)**2)))
+                    quadratic_coeffs(3) = (xy_local(1)/ellipse_coeffs(1))**2._wp + (xy_local(2)/ellipse_coeffs(2))**2._wp - 1._wp
+
+                    ! compute the levelset with the quadratic equation 
+                    levelset%sf(i, j, 0, ib_patch_id) = -0.5_wp * (-quadratic_coeffs(2) + sqrt(quadratic_coeffs(2)**2._wp - 4._wp * quadratic_coeffs(1)*quadratic_coeffs(3))) / quadratic_coeffs(1)
+                end if
+            end do
+        end do
+        $:END_GPU_PARALLEL_LOOP()
+
+    end subroutine s_ellipse_levelset
+
     subroutine s_cuboid_levelset(ib_patch_id, levelset, levelset_norm)
 
         type(levelset_field), intent(INOUT), optional :: levelset
diff --git a/src/common/m_ib_patches.fpp b/src/common/m_ib_patches.fpp
index 18fcf5968e..8468d0b859 100644
--- a/src/common/m_ib_patches.fpp
+++ b/src/common/m_ib_patches.fpp
@@ -773,14 +773,15 @@ contains
 
         integer :: i, j, k !< generic loop iterators
         real(wp), dimension(1:3) :: xy_local !< x and y coordinates in local IB frame
-        real(wp), dimension(1:2) :: length, center !< x and y coordinates in local IB frame
+        real(wp), dimension(1:2) :: ellipse_coeffs !< a and b in the ellipse coefficients
+        real(wp), dimension(1:2) :: center !< x and y coordinates in local IB frame
         real(wp), dimension(1:3, 1:3) :: inverse_rotation
 
         ! Transferring the rectangle's centroid and length information
         center(1) = patch_ib(patch_id)%x_centroid
         center(2) = patch_ib(patch_id)%y_centroid
-        length(1) = patch_ib(patch_id)%length_x
-        length(2) = patch_ib(patch_id)%length_y
+        ellipse_coeffs(1) = 0.5_wp * patch_ib(patch_id)%length_x
+        ellipse_coeffs(2) = 0.5_wp * patch_ib(patch_id)%length_y
         inverse_rotation(:, :) = patch_ib(patch_id)%rotation_matrix_inverse(:, :)
 
         ! Checking whether the rectangle covers a particular cell in the
@@ -788,7 +789,7 @@ contains
         ! to write to that cell. If both queries check out, the primitive
         ! variables of the current patch are assigned to this cell.
         $:GPU_PARALLEL_LOOP(private='[i,j, xy_local]', copy='[ib_markers_sf]',&
-                  & copyin='[patch_id,center,length,inverse_rotation,x_cc,y_cc]', collapse=2)
+                  & copyin='[patch_id,center,ellipse_coeffs,inverse_rotation,x_cc,y_cc]', collapse=2)
         do j = 0, n
             do i = 0, m
                 ! get the x and y coordinates in the local IB frame
@@ -796,7 +797,7 @@ contains
                 xy_local = matmul(inverse_rotation, xy_local)
 
                 ! Ellipse condition (x/a)^2 + (y/b)^2 <= 1
-                if ((xy_local(1)/length(1))**2 + (xy_local(1)/length(1))**2) then
+                if ((xy_local(1)/ellipse_coeffs(1))**2 + (xy_local(2)/ellipse_coeffs(2))**2 <= 1._wp) then
                     ! Updating the patch identities bookkeeping variable
                     ib_markers_sf(i, j, 0) = patch_id
                 end if
diff --git a/src/pre_process/m_check_ib_patches.fpp b/src/pre_process/m_check_ib_patches.fpp
index 7e1f9aa1d7..19493814e5 100644
--- a/src/pre_process/m_check_ib_patches.fpp
+++ b/src/pre_process/m_check_ib_patches.fpp
@@ -62,6 +62,8 @@ contains
                 else if (patch_ib(i)%geometry == 5 .or. &
                          patch_ib(i)%geometry == 12) then
                     call s_check_model_ib_patch_geometry(i)
+                else if (patch_ib(i)%geometry == 6) then
+                    print *, "Ellipse Patch"
                 else
                     call s_prohibit_abort("Invalid IB patch", &
                                           "patch_ib("//trim(iStr)//")%geometry must be "// &

From 2f9b1beac4c083033fc8475f4568725683ed573f Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Fri, 12 Dec 2025 16:51:26 -0500
Subject: [PATCH 03/34] Added an ellipse immersed boundary patch

---
 examples/2D_ibm_ellipse/case.py   | 97 +++++++++++++++++++++++++++++++
 src/common/m_compute_levelset.fpp |  2 +-
 2 files changed, 98 insertions(+), 1 deletion(-)
 create mode 100644 examples/2D_ibm_ellipse/case.py

diff --git a/examples/2D_ibm_ellipse/case.py b/examples/2D_ibm_ellipse/case.py
new file mode 100644
index 0000000000..1c5d8052f7
--- /dev/null
+++ b/examples/2D_ibm_ellipse/case.py
@@ -0,0 +1,97 @@
+import json
+import math
+
+Mu = 1.84e-05
+gam_a = 1.4
+
+# Configuring case dictionary
+print(
+    json.dumps(
+        {
+            # Logistics
+            "run_time_info": "T",
+            # Computational Domain Parameters
+            # For these computations, the cylinder is placed at the (0,0,0)
+            # domain origin.
+            # axial direction
+            "x_domain%beg": 0.0e00,
+            "x_domain%end": 6.0e-03,
+            # r direction
+            "y_domain%beg": 0.0e00,
+            "y_domain%end": 6.0e-03,
+            "cyl_coord": "F",
+            "m": 250,
+            "n": 250,
+            "p": 0,
+            "dt": 0.5e-5,
+            "t_step_start": 0,
+            "t_step_stop": 1000,  # 3000
+            "t_step_save": 10,  # 10
+            # Simulation Algorithm Parameters
+            # Only one patches are necessary, the air tube
+            "num_patches": 1,
+            # Use the 5 equation model
+            "model_eqns": 2,
+            "alt_soundspeed": "F",
+            # One fluids: air
+            "num_fluids": 1,
+            # time step
+            "mpp_lim": "F",
+            # Correct errors when computing speed of sound
+            "mixture_err": "T",
+            # Use TVD RK3 for time marching
+            "time_stepper": 3,
+            # Use WENO5
+            "weno_order": 5,
+            "weno_eps": 1.0e-16,
+            "weno_Re_flux": "T",
+            "weno_avg": "T",
+            "avg_state": 2,
+            "mapped_weno": "T",
+            "null_weights": "F",
+            "mp_weno": "T",
+            "riemann_solver": 2,
+            "wave_speeds": 1,
+            # We use ghost-cell
+            "bc_x%beg": -3,
+            "bc_x%end": -3,
+            "bc_y%beg": -3,
+            "bc_y%end": -3,
+            # Set IB to True and add 1 patch
+            "ib": "T",
+            "num_ibs": 1,
+            "viscous": "T",
+            # Formatted Database Files Structure Parameters
+            "format": 1,
+            "precision": 2,
+            "prim_vars_wrt": "T",
+            "E_wrt": "T",
+            "parallel_io": "T",
+            # Patch: Constant Tube filled with air
+            # Specify the cylindrical air tube grid geometry
+            "patch_icpp(1)%geometry": 3,
+            "patch_icpp(1)%x_centroid": 3.0e-03,
+            # Uniform medium density, centroid is at the center of the domain
+            "patch_icpp(1)%y_centroid": 3.0e-03,
+            "patch_icpp(1)%length_x": 6.0e-03,
+            "patch_icpp(1)%length_y": 6.0e-03,
+            # Specify the patch primitive variables
+            "patch_icpp(1)%vel(1)": 0.05e00,
+            "patch_icpp(1)%vel(2)": 0.0e00,
+            "patch_icpp(1)%pres": 1.0e00,
+            "patch_icpp(1)%alpha_rho(1)": 1.0e00,
+            "patch_icpp(1)%alpha(1)": 1.0e00,
+            # Patch: Cylinder Immersed Boundary
+            "patch_ib(1)%geometry": 6,
+            "patch_ib(1)%x_centroid": 1.5e-03,
+            "patch_ib(1)%y_centroid": 3.0e-03,
+            "patch_ib(1)%length_x": 0.4e-03,
+            "patch_ib(1)%length_y": 0.2e-03,
+            "patch_ib(1)%slip": "F",
+            # Fluids Physical Parameters
+            "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
+            "fluid_pp(1)%pi_inf": 0,
+            "fluid_pp(1)%Re(1)": 2500000,
+        }
+    )
+)
diff --git a/src/common/m_compute_levelset.fpp b/src/common/m_compute_levelset.fpp
index 5346eb1b8b..69ddda5fd5 100644
--- a/src/common/m_compute_levelset.fpp
+++ b/src/common/m_compute_levelset.fpp
@@ -384,7 +384,7 @@ contains
                     quadratic_coeffs(2) = 2._wp * ((xy_local(1)*normal_vector(1)/(ellipse_coeffs(1)**2)) + (xy_local(2)*normal_vector(2)/(ellipse_coeffs(2)**2)))
                     quadratic_coeffs(3) = (xy_local(1)/ellipse_coeffs(1))**2._wp + (xy_local(2)/ellipse_coeffs(2))**2._wp - 1._wp
 
-                    ! compute the levelset with the quadratic equation 
+                    ! compute the levelset with the quadratic equation [ -B + sqrt(B^2 - 4AC) ] / 2A
                     levelset%sf(i, j, 0, ib_patch_id) = -0.5_wp * (-quadratic_coeffs(2) + sqrt(quadratic_coeffs(2)**2._wp - 4._wp * quadratic_coeffs(1)*quadratic_coeffs(3))) / quadratic_coeffs(1)
                 end if
             end do

From 693354f04564e15ed3855d5dbbbe7e9390bcd1f1 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Wed, 17 Dec 2025 16:58:58 -0500
Subject: [PATCH 04/34] added viscous stress tensor calculation

---
 src/simulation/m_ibm.fpp           | 12 ++++--
 src/simulation/m_rhs.fpp           |  4 +-
 src/simulation/m_time_steppers.fpp |  2 +-
 src/simulation/m_viscous.fpp       | 64 ++++++++++++++++++++++++++++--
 4 files changed, 73 insertions(+), 9 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 048032b9ae..986fa5029e 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -997,7 +997,7 @@ contains
     ! compute the surface integrals of the IB via a volume integraion method described in
     ! "A coupled IBM/Euler-Lagrange framework for simulating shock-induced particle size segregation"
     ! by Archana Sridhar and Jesse Capecelatro
-    subroutine s_compute_ib_forces(pressure)
+    subroutine s_compute_ib_forces(pressure, velocities, dynamic_viscosity, bulk_viscosity)
 
         ! real(wp), dimension(idwbuff(1)%beg:idwbuff(1)%end, &
         !             idwbuff(2)%beg:idwbuff(2)%end, &
@@ -1006,14 +1006,14 @@ contains
 
         integer :: i, j, k, l, ib_idx
         real(wp), dimension(num_ibs, 3) :: forces, torques
+        real(wp), dimension(1:3, 1:3) :: viscous_stress_tensor
         real(wp), dimension(1:3) :: pressure_divergence, radial_vector, local_torque_contribution
         real(wp) :: cell_volume, dx, dy, dz
 
         forces = 0._wp
         torques = 0._wp
 
-        ! TODO :: This is currently only valid inviscid, and needs to be extended to add viscocity
-        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,pressure_divergence,cell_volume,local_torque_contribution, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib]', collapse=3)
+        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,pressure_divergence,cell_volume,local_torque_contribution, viscous_stress_tensor, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib]', collapse=3)
         do i = 0, m
             do j = 0, n
                 do k = 0, p
@@ -1046,6 +1046,12 @@ contains
                             ! Update the force values atomically to prevent race conditions
                             call s_cross_product(radial_vector, pressure_divergence, local_torque_contribution) ! separate out to make atomics safe
                             local_torque_contribution = local_torque_contribution*cell_volume
+
+                            ! get the viscous stress and add its contribution
+                            if (viscous) then
+                                s_compute_viscous_stress_tensor(viscous_stress_tensor, velocities, dynamic_viscosity, bulk_viscosity, i, j, k)
+                            end if
+
                             do l = 1, 3
                                 $:GPU_ATOMIC(atomic='update')
                                 forces(ib_idx, l) = forces(ib_idx, l) - (pressure_divergence(l)*cell_volume)
diff --git a/src/simulation/m_rhs.fpp b/src/simulation/m_rhs.fpp
index 47fa433ca9..78570fc2ff 100644
--- a/src/simulation/m_rhs.fpp
+++ b/src/simulation/m_rhs.fpp
@@ -1635,14 +1635,14 @@ contains
             if (cyl_coord .and. ((bc_y%beg == -2) .or. (bc_y%beg == -14))) then
                 if (viscous) then
                     if (p > 0) then
-                        call s_compute_viscous_stress_tensor(q_prim_vf, &
+                        call s_compute_viscous_stress_cylindrical_boundary(q_prim_vf, &
                                                              dq_prim_dx_vf(mom_idx%beg:mom_idx%end), &
                                                              dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
                                                              dq_prim_dz_vf(mom_idx%beg:mom_idx%end), &
                                                              tau_Re_vf, &
                                                              idwbuff(1), idwbuff(2), idwbuff(3))
                     else
-                        call s_compute_viscous_stress_tensor(q_prim_vf, &
+                        call s_compute_viscous_stress_cylindrical_boundary(q_prim_vf, &
                                                              dq_prim_dx_vf(mom_idx%beg:mom_idx%end), &
                                                              dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
                                                              dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
diff --git a/src/simulation/m_time_steppers.fpp b/src/simulation/m_time_steppers.fpp
index f17689d6bc..cfd8241395 100644
--- a/src/simulation/m_time_steppers.fpp
+++ b/src/simulation/m_time_steppers.fpp
@@ -627,7 +627,7 @@ contains
 
                             if (patch_ib(i)%moving_ibm == 2) then ! if we are using two-way coupling, apply force and torque
                                 ! compute the force and torque on the IB from the fluid
-                                call s_compute_ib_forces(q_prim_vf(E_idx))
+                                call s_compute_ib_forces(q_prim_vf(E_idx), q_prim_vf(momxb:momxb+2)%sf)
 
                                 ! update the velocity from the force value
                                 patch_ib(i)%vel = patch_ib(i)%vel + rk_coef(s, 3)*dt*(patch_ib(i)%force/patch_ib(i)%mass)/rk_coef(s, 4)
diff --git a/src/simulation/m_viscous.fpp b/src/simulation/m_viscous.fpp
index 1b01e09404..50c3b073e2 100644
--- a/src/simulation/m_viscous.fpp
+++ b/src/simulation/m_viscous.fpp
@@ -21,7 +21,7 @@ module m_viscous
     use m_finite_differences
 
     private; public s_get_viscous, &
- s_compute_viscous_stress_tensor, &
+    s_compute_viscous_stress_cylindrical_boundary, &
  s_initialize_viscous_module, &
  s_reconstruct_cell_boundary_values_visc_deriv, &
  s_finalize_viscous_module
@@ -60,7 +60,7 @@ contains
     !  @param grad_x_vf Cell-average primitive variable derivatives, x-dir
     !  @param grad_y_vf Cell-average primitive variable derivatives, y-dir
     !  @param grad_z_vf Cell-average primitive variable derivatives, z-dir
-    subroutine s_compute_viscous_stress_tensor(q_prim_vf, grad_x_vf, grad_y_vf, grad_z_vf, &
+    subroutine s_compute_viscous_stress_cylindrical_boundary(q_prim_vf, grad_x_vf, grad_y_vf, grad_z_vf, &
                                                tau_Re_vf, &
                                                ix, iy, iz)
 
@@ -518,7 +518,7 @@ contains
                 $:END_GPU_PARALLEL_LOOP()
             end if
         #:endif
-    end subroutine s_compute_viscous_stress_tensor
+    end subroutine s_compute_viscous_stress_cylindrical_boundary
 
     !>  Computes viscous terms
     !!  @param q_cons_vf Cell-averaged conservative variables
@@ -1511,6 +1511,64 @@ contains
 
     end subroutine s_compute_fd_gradient
 
+    ! computes the viscous stress tensor at a particule i, j, k element
+    subroutine s_compute_viscous_stress_tensor(viscous_stress_tensor, velocities, dynamic_viscosity, bulk_viscosity, i, j, k)
+      $:GPU_ROUTINE(parallelism='[seq]')
+
+      real(wp), dimension(1:3, 1:3), intent(inout) :: viscous_stress_tensor
+      type(scalar_field), dimension(1:3), intent(in) :: velocities
+      real(wp), intent(in) :: dynamic_viscosity, bulk_viscosity
+      integer, intent(in) :: i, j, k
+
+      real(wp), dimension(1:3, 1:3) :: velocity_gradient_tensor, shear_strain_tensor
+      real(wp), dimension(1:3) :: dx
+      real(wp) :: divergence
+      integer :: l, q ! iterators
+
+      ! zero the viscous stress, collection of velocity diriviatives, and spacial finite differences
+      viscous_stress_tensor = 0._wp
+      shear_strain_tensor = 0._wp
+      velocity_gradient_tensor = 0._wp
+      dx = 0._wp
+
+      ! get the change in x used in the finite difference equaiont
+      dx(1) = 0.5_wp * (x_cc(i+1) - x_cc(i-1))
+      dx(2) = 0.5_wp * (y_cc(j+1) - y_cc(j-1))
+      if (num_dims == 3) then
+          dx(3) = 0.5_wp * (z_cc(k+1) - z_cc(k-1))
+      end if
+
+      ! compute the velocity gradient tensor
+      do l = 1:num_dims
+          velocity_gradient_tensor(l,1) = (velocities(l)%sf(i+1, j, k) - velocities(l)%sf(i-1, j, k)) / (2._wp * dx(1)) 
+          velocity_gradient_tensor(l,2) = (velocities(l)%sf(i, j+1, k) - velocities(l)%sf(i, j-1, k)) / (2._wp * dx(2))
+          if (num_dims == 3) then
+              velocity_gradient_tensor(l,3) = (velocities(l)%sf(i, j, k+1) - velocities(l)%sf(i, j, k-1)) / (2._wp * dx(3)) 
+          end if
+      end do
+
+      ! compute divergence
+      divergence = velocity_gradient_tensor(1, 1) + velocity_gradient_tensor(2, 2) + velocity_gradient_tensor(3, 3)
+
+      ! set up the shear stress tensor
+      do l = 1:num_dims
+          do q = 1:num_dims
+              shear_strain_tensor(l, q) = 0.5_wp * (velocity_gradient_tensor(l,q) + velocity_gradient_tensor(q,l))
+          end do
+      end do
+
+      ! populate the viscous_stress_tensor
+      do l = 1num_dims
+        do q = 1:num_dims
+          viscous_stress_tensor(l, q) = shear_strain_tensor(l, q)*dynamic_viscosity*2._wp
+          if (l == q) then
+              viscous_stress_tensor(l, q) = viscous_stress_tensor(l, q) + divergence * bulk_viscosity
+          end if
+        end do
+      end do
+
+    end subroutine s_compute_viscous_stress_tensor
+
     impure subroutine s_finalize_viscous_module()
 
         @:DEALLOCATE(Res_viscous)

From 31c9d1a5b754654747fdfbdca43303b3a114ec1e Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Thu, 18 Dec 2025 15:28:51 -0500
Subject: [PATCH 05/34] Finally added the compute from the viscous stress

---
 src/simulation/m_ibm.fpp | 77 +++++++++++++++++++++++++++++++---------
 1 file changed, 60 insertions(+), 17 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 986fa5029e..9f43f44410 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1003,17 +1003,19 @@ contains
         !             idwbuff(2)%beg:idwbuff(2)%end, &
         !             idwbuff(3)%beg:idwbuff(3)%end), intent(in) :: pressure
         type(scalar_field), intent(in) :: pressure
+        type(scalar_field), dimension(1:3), intent(in) :: velocities
+        real(wp), intent(in) :: dynamic_viscosity, bulk_viscosity
 
-        integer :: i, j, k, l, ib_idx
+        integer :: i, j, k, l, q, ib_idx
         real(wp), dimension(num_ibs, 3) :: forces, torques
-        real(wp), dimension(1:3, 1:3) :: viscous_stress_tensor
-        real(wp), dimension(1:3) :: pressure_divergence, radial_vector, local_torque_contribution
+        real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2 ! viscous stress tensor with temp vectors to hold divergence calculations 
+        real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution
         real(wp) :: cell_volume, dx, dy, dz
 
         forces = 0._wp
         torques = 0._wp
 
-        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,pressure_divergence,cell_volume,local_torque_contribution, viscous_stress_tensor, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib]', collapse=3)
+        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,velocities,dynamic_viscosity,bulk_viscosity]', collapse=3)
         do i = 0, m
             do j = 0, n
                 do k = 0, p
@@ -1029,34 +1031,68 @@ contains
                             dx = x_cc(i + 1) - x_cc(i)
                             dy = y_cc(j + 1) - y_cc(j)
 
-                            ! use a finite difference to compute the 2D components of the gradient of the pressure and cell volume
-                            pressure_divergence(1) = (pressure%sf(i + 1, j, k) - pressure%sf(i - 1, j, k))/(2._wp*dx)
-                            pressure_divergence(2) = (pressure%sf(i, j + 1, k) - pressure%sf(i, j - 1, k))/(2._wp*dy)
+                            ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
+                            local_force_contribution(1) = (pressure%sf(i + 1, j, k) - pressure%sf(i - 1, j, k))/(2._wp*dx)
+                            local_force_contribution(2) = (pressure%sf(i, j + 1, k) - pressure%sf(i, j - 1, k))/(2._wp*dy)
                             cell_volume = dx*dy
-
-                            ! add the 3D component, if we are working in 3 dimensions
+                            ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
                             if (num_dims == 3) then
                                 dz = z_cc(k + 1) - z_cc(k)
-                                pressure_divergence(3) = (pressure%sf(i, j, k + 1) - pressure%sf(i, j, k - 1))/(2._wp*dz)
+                                local_force_contribution(3) = (pressure%sf(i, j, k + 1) - pressure%sf(i, j, k - 1))/(2._wp*dz)
                                 cell_volume = cell_volume*dz
                             else
-                                pressure_divergence(3) = 0._wp
+                              local_force_contribution(3) = 0._wp
                             end if
 
                             ! Update the force values atomically to prevent race conditions
-                            call s_cross_product(radial_vector, pressure_divergence, local_torque_contribution) ! separate out to make atomics safe
-                            local_torque_contribution = local_torque_contribution*cell_volume
+                            call s_cross_product(radial_vector, local_force_contribution, local_torque_contribution)
 
-                            ! get the viscous stress and add its contribution
+                            ! get the viscous stress and add its contribution if that is considered
+                            ! TODO :: This is really bad code
                             if (viscous) then
-                                s_compute_viscous_stress_tensor(viscous_stress_tensor, velocities, dynamic_viscosity, bulk_viscosity, i, j, k)
+                                ! get the linear force component first
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, velocities, dynamic_viscosity, bulk_viscosity, i-1, j, k)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, velocities, dynamic_viscosity, bulk_viscosity, i+1, j, k)
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
+                                local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
+                                do l = 1, 3
+                                    ! take the cross products for the torque componenet
+                                    call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                                    call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                                end do
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross products
+                                local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
+                                
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, velocities, dynamic_viscosity, bulk_viscosity, i, j-1, k)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, velocities, dynamic_viscosity, bulk_viscosity, i, j+1, k)
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div) / (2._wp * dy)
+                                local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
+                                do l = 1, 3
+                                    call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                                    call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                                end do
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
+                                local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3)
+
+                                if (dum_dims == 3) then
+                                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, velocities, dynamic_viscosity, bulk_viscosity, i, j, k-1)
+                                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, velocities, dynamic_viscosity, bulk_viscosity, i, j, k+1)
+                                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
+                                    local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
+                                    do l = 1, 3
+                                        call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                                        call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                                    end do
+                                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
+                                    local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3)
+                                end if
                             end if
 
                             do l = 1, 3
                                 $:GPU_ATOMIC(atomic='update')
-                                forces(ib_idx, l) = forces(ib_idx, l) - (pressure_divergence(l)*cell_volume)
+                                forces(ib_idx, l) = forces(ib_idx, l) - (local_force_contribution(l)*cell_volume)
                                 $:GPU_ATOMIC(atomic='update')
-                                torques(ib_idx, l) = torques(ib_idx, l) - local_torque_contribution(l)
+                                torques(ib_idx, l) = torques(ib_idx, l) - local_torque_contribution(l)*cell_volume
                             end do
                         end if
                     end if
@@ -1069,6 +1105,13 @@ contains
         call s_mpi_allreduce_vectors_sum(forces, forces, num_ibs, 3)
         call s_mpi_allreduce_vectors_sum(torques, torques, num_ibs, 3)
 
+        ! consider gravity after reducing to avoid double counting
+        if (body_forces) then
+            do i = 1, num_ibs
+                forces(i, 2) = forces(i, 2) - 9.8*patch_ib(ib_idx)%mass ! -9.8 m/s/s acceleration in the y direction
+            end do
+        end if
+
         ! apply the summed forces
         do i = 1, num_ibs
             patch_ib(i)%force(:) = forces(i, :)

From 402bfe2a939d52085b0e9ba2ac0429c420c8ef19 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Thu, 18 Dec 2025 15:35:22 -0500
Subject: [PATCH 06/34] Added body forces

---
 src/simulation/m_ibm.fpp | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 9f43f44410..406f4eac0c 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1105,12 +1105,19 @@ contains
         call s_mpi_allreduce_vectors_sum(forces, forces, num_ibs, 3)
         call s_mpi_allreduce_vectors_sum(torques, torques, num_ibs, 3)
 
-        ! consider gravity after reducing to avoid double counting
-        if (body_forces) then
-            do i = 1, num_ibs
-                forces(i, 2) = forces(i, 2) - 9.8*patch_ib(ib_idx)%mass ! -9.8 m/s/s acceleration in the y direction
-            end do
-        end if
+        ! consider body forces after reducing to avoid double counting
+        
+        do i = 1, num_ibs
+          if (bf_x) then
+              forces(i, 1) = forces(i, 1) + accel_bf(1)*patch_ib(ib_idx)%mass
+          end if
+          if (bf_y) then
+              forces(i, 2) = forces(i, 3) + accel_bf(2)*patch_ib(ib_idx)%mass
+          end if
+          if (bf_z) then
+              forces(i, 3) = forces(i, 3) + accel_bf(3)*patch_ib(ib_idx)%mass
+          end if
+        end do
 
         ! apply the summed forces
         do i = 1, num_ibs

From 82ce8beb447718f4c4bcbde619c144b815e5c5e2 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Thu, 18 Dec 2025 16:08:09 -0500
Subject: [PATCH 07/34] compiles

---
 src/simulation/m_ibm.fpp           | 29 +++++++++++++-------------
 src/simulation/m_time_steppers.fpp |  2 +-
 src/simulation/m_viscous.fpp       | 33 +++++++++++++++---------------
 3 files changed, 33 insertions(+), 31 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 406f4eac0c..e92575be25 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -26,6 +26,8 @@ module m_ibm
 
     use m_ib_patches
 
+    use m_viscous
+
     implicit none
 
     private :: s_compute_image_points, &
@@ -997,13 +999,12 @@ contains
     ! compute the surface integrals of the IB via a volume integraion method described in
     ! "A coupled IBM/Euler-Lagrange framework for simulating shock-induced particle size segregation"
     ! by Archana Sridhar and Jesse Capecelatro
-    subroutine s_compute_ib_forces(pressure, velocities, dynamic_viscosity, bulk_viscosity)
+    subroutine s_compute_ib_forces(q_prim_vf, dynamic_viscosity, bulk_viscosity)
 
         ! real(wp), dimension(idwbuff(1)%beg:idwbuff(1)%end, &
         !             idwbuff(2)%beg:idwbuff(2)%end, &
         !             idwbuff(3)%beg:idwbuff(3)%end), intent(in) :: pressure
-        type(scalar_field), intent(in) :: pressure
-        type(scalar_field), dimension(1:3), intent(in) :: velocities
+        type(scalar_field), dimension(1:sys_size), intent(in) :: q_prim_vf
         real(wp), intent(in) :: dynamic_viscosity, bulk_viscosity
 
         integer :: i, j, k, l, q, ib_idx
@@ -1015,7 +1016,7 @@ contains
         forces = 0._wp
         torques = 0._wp
 
-        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,velocities,dynamic_viscosity,bulk_viscosity]', collapse=3)
+        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
         do i = 0, m
             do j = 0, n
                 do k = 0, p
@@ -1032,13 +1033,13 @@ contains
                             dy = y_cc(j + 1) - y_cc(j)
 
                             ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
-                            local_force_contribution(1) = (pressure%sf(i + 1, j, k) - pressure%sf(i - 1, j, k))/(2._wp*dx)
-                            local_force_contribution(2) = (pressure%sf(i, j + 1, k) - pressure%sf(i, j - 1, k))/(2._wp*dy)
+                            local_force_contribution(1) = (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx)
+                            local_force_contribution(2) = (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
                             cell_volume = dx*dy
                             ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
                             if (num_dims == 3) then
                                 dz = z_cc(k + 1) - z_cc(k)
-                                local_force_contribution(3) = (pressure%sf(i, j, k + 1) - pressure%sf(i, j, k - 1))/(2._wp*dz)
+                                local_force_contribution(3) = (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
                                 cell_volume = cell_volume*dz
                             else
                               local_force_contribution(3) = 0._wp
@@ -1051,8 +1052,8 @@ contains
                             ! TODO :: This is really bad code
                             if (viscous) then
                                 ! get the linear force component first
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, velocities, dynamic_viscosity, bulk_viscosity, i-1, j, k)
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, velocities, dynamic_viscosity, bulk_viscosity, i+1, j, k)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i-1, j, k)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, bulk_viscosity, i+1, j, k)
                                 viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
                                 local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
                                 do l = 1, 3
@@ -1063,8 +1064,8 @@ contains
                                 viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross products
                                 local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
                                 
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, velocities, dynamic_viscosity, bulk_viscosity, i, j-1, k)
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, velocities, dynamic_viscosity, bulk_viscosity, i, j+1, k)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j-1, k)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j+1, k)
                                 viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div) / (2._wp * dy)
                                 local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
                                 do l = 1, 3
@@ -1074,9 +1075,9 @@ contains
                                 viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
                                 local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3)
 
-                                if (dum_dims == 3) then
-                                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, velocities, dynamic_viscosity, bulk_viscosity, i, j, k-1)
-                                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, velocities, dynamic_viscosity, bulk_viscosity, i, j, k+1)
+                                if (num_dims == 3) then
+                                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j, k-1)
+                                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j, k+1)
                                     viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
                                     local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
                                     do l = 1, 3
diff --git a/src/simulation/m_time_steppers.fpp b/src/simulation/m_time_steppers.fpp
index cfd8241395..959629cfd0 100644
--- a/src/simulation/m_time_steppers.fpp
+++ b/src/simulation/m_time_steppers.fpp
@@ -627,7 +627,7 @@ contains
 
                             if (patch_ib(i)%moving_ibm == 2) then ! if we are using two-way coupling, apply force and torque
                                 ! compute the force and torque on the IB from the fluid
-                                call s_compute_ib_forces(q_prim_vf(E_idx), q_prim_vf(momxb:momxb+2)%sf)
+                                call s_compute_ib_forces(q_prim_vf, fluid_pp(1)%Re(1), fluid_pp(1)%Re(2))
 
                                 ! update the velocity from the force value
                                 patch_ib(i)%vel = patch_ib(i)%vel + rk_coef(s, 3)*dt*(patch_ib(i)%force/patch_ib(i)%mass)/rk_coef(s, 4)
diff --git a/src/simulation/m_viscous.fpp b/src/simulation/m_viscous.fpp
index 50c3b073e2..41d7692229 100644
--- a/src/simulation/m_viscous.fpp
+++ b/src/simulation/m_viscous.fpp
@@ -24,7 +24,8 @@ module m_viscous
     s_compute_viscous_stress_cylindrical_boundary, &
  s_initialize_viscous_module, &
  s_reconstruct_cell_boundary_values_visc_deriv, &
- s_finalize_viscous_module
+ s_finalize_viscous_module, &
+ s_compute_viscous_stress_tensor
 
     type(int_bounds_info) :: iv
     type(int_bounds_info) :: is1_viscous, is2_viscous, is3_viscous
@@ -1512,11 +1513,11 @@ contains
     end subroutine s_compute_fd_gradient
 
     ! computes the viscous stress tensor at a particule i, j, k element
-    subroutine s_compute_viscous_stress_tensor(viscous_stress_tensor, velocities, dynamic_viscosity, bulk_viscosity, i, j, k)
+    subroutine s_compute_viscous_stress_tensor(viscous_stress_tensor, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j, k)
       $:GPU_ROUTINE(parallelism='[seq]')
 
       real(wp), dimension(1:3, 1:3), intent(inout) :: viscous_stress_tensor
-      type(scalar_field), dimension(1:3), intent(in) :: velocities
+      type(scalar_field), dimension(1:sys_size), intent(in) :: q_prim_vf
       real(wp), intent(in) :: dynamic_viscosity, bulk_viscosity
       integer, intent(in) :: i, j, k
 
@@ -1539,11 +1540,11 @@ contains
       end if
 
       ! compute the velocity gradient tensor
-      do l = 1:num_dims
-          velocity_gradient_tensor(l,1) = (velocities(l)%sf(i+1, j, k) - velocities(l)%sf(i-1, j, k)) / (2._wp * dx(1)) 
-          velocity_gradient_tensor(l,2) = (velocities(l)%sf(i, j+1, k) - velocities(l)%sf(i, j-1, k)) / (2._wp * dx(2))
+      do l = 1, num_dims
+          velocity_gradient_tensor(l,1) = (q_prim_vf(momxb+l)%sf(i+1, j, k) - q_prim_vf(momxb+l)%sf(i-1, j, k)) / (2._wp * dx(1)) 
+          velocity_gradient_tensor(l,2) = (q_prim_vf(momxb+l)%sf(i, j+1, k) - q_prim_vf(momxb+l)%sf(i, j-1, k)) / (2._wp * dx(2))
           if (num_dims == 3) then
-              velocity_gradient_tensor(l,3) = (velocities(l)%sf(i, j, k+1) - velocities(l)%sf(i, j, k-1)) / (2._wp * dx(3)) 
+              velocity_gradient_tensor(l,3) = (q_prim_vf(momxb+l)%sf(i, j, k+1) - q_prim_vf(momxb+l)%sf(i, j, k-1)) / (2._wp * dx(3)) 
           end if
       end do
 
@@ -1551,20 +1552,20 @@ contains
       divergence = velocity_gradient_tensor(1, 1) + velocity_gradient_tensor(2, 2) + velocity_gradient_tensor(3, 3)
 
       ! set up the shear stress tensor
-      do l = 1:num_dims
-          do q = 1:num_dims
+      do l = 1, num_dims
+          do q = 1, num_dims
               shear_strain_tensor(l, q) = 0.5_wp * (velocity_gradient_tensor(l,q) + velocity_gradient_tensor(q,l))
           end do
       end do
 
       ! populate the viscous_stress_tensor
-      do l = 1num_dims
-        do q = 1:num_dims
-          viscous_stress_tensor(l, q) = shear_strain_tensor(l, q)*dynamic_viscosity*2._wp
-          if (l == q) then
-              viscous_stress_tensor(l, q) = viscous_stress_tensor(l, q) + divergence * bulk_viscosity
-          end if
-        end do
+      do l = 1, num_dims
+          do q = 1, num_dims
+              viscous_stress_tensor(l, q) = shear_strain_tensor(l, q)*dynamic_viscosity*2._wp
+              if (l == q) then
+                  viscous_stress_tensor(l, q) = viscous_stress_tensor(l, q) + divergence * bulk_viscosity
+              end if
+          end do
       end do
 
     end subroutine s_compute_viscous_stress_tensor

From eaa9e36c53cdc9daa83f900ce5979fc9f34ee650 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Thu, 18 Dec 2025 17:12:11 -0500
Subject: [PATCH 08/34] Getting errors with viscosity turned on. Going to take
 a break for the day.

---
 src/simulation/m_ibm.fpp     | 6 ++++--
 src/simulation/m_viscous.fpp | 6 +++---
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index e92575be25..adde9862a0 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1016,6 +1016,7 @@ contains
         forces = 0._wp
         torques = 0._wp
 
+        ! TODO :: Change this to a loop over ghost points
         $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
         do i = 0, m
             do j = 0, n
@@ -1050,7 +1051,8 @@ contains
 
                             ! get the viscous stress and add its contribution if that is considered
                             ! TODO :: This is really bad code
-                            if (viscous) then
+                            ! if (viscous) then
+                            if (.false.) then
                                 ! get the linear force component first
                                 call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i-1, j, k)
                                 call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, bulk_viscosity, i+1, j, k)
@@ -1061,7 +1063,7 @@ contains
                                     call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
                                     call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
                                 end do
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross products
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
                                 local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
                                 
                                 call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j-1, k)
diff --git a/src/simulation/m_viscous.fpp b/src/simulation/m_viscous.fpp
index 41d7692229..fdb201ee19 100644
--- a/src/simulation/m_viscous.fpp
+++ b/src/simulation/m_viscous.fpp
@@ -1541,10 +1541,10 @@ contains
 
       ! compute the velocity gradient tensor
       do l = 1, num_dims
-          velocity_gradient_tensor(l,1) = (q_prim_vf(momxb+l)%sf(i+1, j, k) - q_prim_vf(momxb+l)%sf(i-1, j, k)) / (2._wp * dx(1)) 
-          velocity_gradient_tensor(l,2) = (q_prim_vf(momxb+l)%sf(i, j+1, k) - q_prim_vf(momxb+l)%sf(i, j-1, k)) / (2._wp * dx(2))
+          velocity_gradient_tensor(l,1) = (q_prim_vf(momxb+l-1)%sf(i+1, j, k) - q_prim_vf(momxb+l-1)%sf(i-1, j, k)) / (2._wp * dx(1)) 
+          velocity_gradient_tensor(l,2) = (q_prim_vf(momxb+l-1)%sf(i, j+1, k) - q_prim_vf(momxb+l-1)%sf(i, j-1, k)) / (2._wp * dx(2))
           if (num_dims == 3) then
-              velocity_gradient_tensor(l,3) = (q_prim_vf(momxb+l)%sf(i, j, k+1) - q_prim_vf(momxb+l)%sf(i, j, k-1)) / (2._wp * dx(3)) 
+              velocity_gradient_tensor(l,3) = (q_prim_vf(momxb+l-1)%sf(i, j, k+1) - q_prim_vf(momxb+l-1)%sf(i, j, k-1)) / (2._wp * dx(3)) 
           end if
       end do
 

From 66aa089b2921eecc4690d21f0ba73fc38bba81a6 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 19 Dec 2025 09:18:19 -0500
Subject: [PATCH 09/34] new viscous example

---
 examples/2D_mibm_falling_sediment/case.py | 101 ++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 examples/2D_mibm_falling_sediment/case.py

diff --git a/examples/2D_mibm_falling_sediment/case.py b/examples/2D_mibm_falling_sediment/case.py
new file mode 100644
index 0000000000..f61dd9293d
--- /dev/null
+++ b/examples/2D_mibm_falling_sediment/case.py
@@ -0,0 +1,101 @@
+import json
+import math
+
+Mu = 1.84e-05
+gam_a = 1.4
+
+# Configuring case dictionary
+print(
+    json.dumps(
+        {
+            # Logistics
+            "run_time_info": "T",
+            # Computational Domain Parameters
+            # For these computations, the cylinder is placed at the (0,0,0)
+            # domain origin.
+            # axial direction
+            "x_domain%beg": 0.0e00,
+            "x_domain%end": 6.0e-03,
+            # r direction
+            "y_domain%beg": 0.0e00,
+            "y_domain%end": 6.0e-03,
+            "cyl_coord": "F",
+            "m": 250,
+            "n": 250,
+            "p": 0,
+            "dt": 0.5e-5,
+            "t_step_start": 0,
+            "t_step_stop": 5000,  # 3000
+            "t_step_save": 50,  # 10
+            # Simulation Algorithm Parameters
+            # Only one patches are necessary, the air tube
+            "num_patches": 1,
+            # Use the 5 equation model
+            "model_eqns": 2,
+            "alt_soundspeed": "F",
+            # One fluids: air
+            "num_fluids": 1,
+            # time step
+            "mpp_lim": "F",
+            # Correct errors when computing speed of sound
+            "mixture_err": "T",
+            # Use TVD RK3 for time marching
+            "time_stepper": 3,
+            # Use WENO5
+            "weno_order": 5,
+            "weno_eps": 1.0e-16,
+            "weno_Re_flux": "T",
+            "weno_avg": "T",
+            "avg_state": 2,
+            "mapped_weno": "T",
+            "null_weights": "F",
+            "mp_weno": "T",
+            "riemann_solver": 2,
+            "wave_speeds": 1,
+            # We use ghost-cell
+            "bc_x%beg": -3,
+            "bc_x%end": -3,
+            "bc_y%beg": -3,
+            "bc_y%end": -3,
+            # Set IB to True and add 1 patch
+            "ib": "T",
+            "num_ibs": 1,
+            "viscous": "T",
+            # Formatted Database Files Structure Parameters
+            "format": 1,
+            "precision": 2,
+            "prim_vars_wrt": "T",
+            "E_wrt": "T",
+            "parallel_io": "T",
+            # Patch: Constant Tube filled with air
+            # Specify the cylindrical air tube grid geometry
+            "patch_icpp(1)%geometry": 3,
+            "patch_icpp(1)%x_centroid": 3.0e-03,
+            # Uniform medium density, centroid is at the center of the domain
+            "patch_icpp(1)%y_centroid": 3.0e-03,
+            "patch_icpp(1)%length_x": 6.0e-03,
+            "patch_icpp(1)%length_y": 6.0e-03,
+            # Specify the patch primitive variables
+            "patch_icpp(1)%vel(1)": 0.00e00,
+            "patch_icpp(1)%vel(2)": 0.0e00,
+            "patch_icpp(1)%pres": 1.0e00,
+            "patch_icpp(1)%alpha_rho(1)": 1.0e00,
+            "patch_icpp(1)%alpha(1)": 1.0e00,
+            # Patch: Cylinder Immersed Boundary
+            "patch_ib(1)%geometry": 6,
+            "patch_ib(1)%moving_ibm": 2,
+            "patch_ib(1)%x_centroid": 1.5e-03,
+            "patch_ib(1)%y_centroid": 3.0e-03,
+            "patch_ib(1)%length_x": 0.4e-03,
+            "patch_ib(1)%length_y": 0.2e-03,
+            "patch_ib(1)%vel(2)": -0.05e00,
+            "patch_ib(1)%angles(3)": -math.pi / 4.,
+            "patch_ib(1)%mass": 1.0e-6, 
+            "patch_ib(1)%slip": "F",
+            # Fluids Physical Parameters
+            "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
+            "fluid_pp(1)%pi_inf": 0,
+            "fluid_pp(1)%Re(1)": 2500000,
+        }
+    )
+)

From a6c85bb992c64e2d16d003bdf5d005684e3252e4 Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Fri, 19 Dec 2025 11:06:52 -0500
Subject: [PATCH 10/34] Looks like it is approximately working

---
 src/simulation/m_ibm.fpp           | 182 +++++++++++++++--------------
 src/simulation/m_time_steppers.fpp |   2 +-
 src/simulation/m_viscous.fpp       |  28 +++--
 3 files changed, 114 insertions(+), 98 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index adde9862a0..19a91b55c3 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -199,12 +199,23 @@ contains
         type(ghost_point) :: innerp
 
         ! set the Moving IBM interior Pressure Values
-        $:GPU_PARALLEL_LOOP(private='[i,j,k]', copyin='[E_idx]', collapse=3)
+        $:GPU_PARALLEL_LOOP(private='[i,j,k,patch_id,rho]', copyin='[E_idx,momxb]', collapse=3)
         do l = 0, p
             do k = 0, n
                 do j = 0, m
-                    if (ib_markers%sf(j, k, l) /= 0) then
+                    patch_id = ib_markers%sf(j, k, l)
+                    if (patch_id /= 0) then
                         q_prim_vf(E_idx)%sf(j, k, l) = 1._wp
+                        if (patch_ib(patch_id)%moving_ibm > 0._wp) then
+                              rho = 0._wp
+                              do i = 1, num_fluids
+                                  rho = rho + q_prim_vf(contxb+i-1)%sf(j, k, l)
+                              end do
+
+                              do i = 1, num_dims
+                                  q_cons_vf(momxb+i-1)%sf(j, k, l) = patch_ib(patch_id)%vel(i) * rho
+                              end do
+                        end if
                     end if
                 end do
             end do
@@ -999,15 +1010,15 @@ contains
     ! compute the surface integrals of the IB via a volume integraion method described in
     ! "A coupled IBM/Euler-Lagrange framework for simulating shock-induced particle size segregation"
     ! by Archana Sridhar and Jesse Capecelatro
-    subroutine s_compute_ib_forces(q_prim_vf, dynamic_viscosity, bulk_viscosity)
+    subroutine s_compute_ib_forces(q_prim_vf, dynamic_viscosity)
 
         ! real(wp), dimension(idwbuff(1)%beg:idwbuff(1)%end, &
         !             idwbuff(2)%beg:idwbuff(2)%end, &
         !             idwbuff(3)%beg:idwbuff(3)%end), intent(in) :: pressure
         type(scalar_field), dimension(1:sys_size), intent(in) :: q_prim_vf
-        real(wp), intent(in) :: dynamic_viscosity, bulk_viscosity
+        real(wp), intent(in) :: dynamic_viscosity
 
-        integer :: i, j, k, l, q, ib_idx
+        integer :: gp_id, i, j, k, l, q, ib_idx
         real(wp), dimension(num_ibs, 3) :: forces, torques
         real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2 ! viscous stress tensor with temp vectors to hold divergence calculations 
         real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution
@@ -1018,89 +1029,88 @@ contains
 
         ! TODO :: Change this to a loop over ghost points
         $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
-        do i = 0, m
-            do j = 0, n
-                do k = 0, p
-                    ib_idx = ib_markers%sf(i, j, k)
-                    if (ib_idx /= 0) then ! only need to compute the gradient for cells inside a IB
-                        if (patch_ib(ib_idx)%moving_ibm == 2) then ! make sure that this IB has 2-way coupling enabled
-                            ! get the vector pointing to the grid cell from the IB centroid
-                            if (num_dims == 3) then
-                                radial_vector = [x_cc(i), y_cc(j), z_cc(k)] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, patch_ib(ib_idx)%z_centroid]
-                            else
-                                radial_vector = [x_cc(i), y_cc(j), 0._wp] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, 0._wp]
-                            end if
-                            dx = x_cc(i + 1) - x_cc(i)
-                            dy = y_cc(j + 1) - y_cc(j)
-
-                            ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
-                            local_force_contribution(1) = (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx)
-                            local_force_contribution(2) = (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
-                            cell_volume = dx*dy
-                            ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
-                            if (num_dims == 3) then
-                                dz = z_cc(k + 1) - z_cc(k)
-                                local_force_contribution(3) = (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
-                                cell_volume = cell_volume*dz
-                            else
-                              local_force_contribution(3) = 0._wp
-                            end if
+        do gp_id = 1, num_gps
+            i = ghost_points(gp_id)%loc(1)
+            j = ghost_points(gp_id)%loc(2)
+            k = ghost_points(gp_id)%loc(3)
+            ib_idx = ghost_points(gp_id)%ib_patch_id
+            if (ib_idx /= 0 .and. patch_ib(ib_idx)%moving_ibm == 2) then ! only need to compute the gradient for cells inside a IB
+                ! get the vector pointing to the grid cell from the IB centroid
+                if (num_dims == 3) then
+                    radial_vector = [x_cc(i), y_cc(j), z_cc(k)] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, patch_ib(ib_idx)%z_centroid]
+                else
+                    radial_vector = [x_cc(i), y_cc(j), 0._wp] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, 0._wp]
+                end if
+                dx = x_cc(i + 1) - x_cc(i)
+                dy = y_cc(j + 1) - y_cc(j)
+
+                ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
+                local_force_contribution(1) = (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx)
+                local_force_contribution(2) = (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
+                cell_volume = dx*dy
+                ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
+                if (num_dims == 3) then
+                    dz = z_cc(k + 1) - z_cc(k)
+                    local_force_contribution(3) = (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
+                    cell_volume = cell_volume*dz
+                else
+                  local_force_contribution(3) = 0._wp
+                end if
 
-                            ! Update the force values atomically to prevent race conditions
-                            call s_cross_product(radial_vector, local_force_contribution, local_torque_contribution)
-
-                            ! get the viscous stress and add its contribution if that is considered
-                            ! TODO :: This is really bad code
-                            ! if (viscous) then
-                            if (.false.) then
-                                ! get the linear force component first
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i-1, j, k)
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, bulk_viscosity, i+1, j, k)
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
-                                local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
-                                do l = 1, 3
-                                    ! take the cross products for the torque componenet
-                                    call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                                    call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
-                                end do
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
-                                local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
-                                
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j-1, k)
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j+1, k)
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div) / (2._wp * dy)
-                                local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
-                                do l = 1, 3
-                                    call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                                    call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
-                                end do
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
-                                local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3)
-
-                                if (num_dims == 3) then
-                                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j, k-1)
-                                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j, k+1)
-                                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
-                                    local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
-                                    do l = 1, 3
-                                        call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                                        call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
-                                    end do
-                                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
-                                    local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3)
-                                end if
-                            end if
+                ! Update the force values atomically to prevent race conditions
+                call s_cross_product(radial_vector, local_force_contribution, local_torque_contribution)
+
+                ! get the viscous stress and add its contribution if that is considered
+                ! TODO :: This is really bad code
+                ! if (viscous) then
+                if (viscous) then
+                    ! get the linear force component first
+                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i-1, j, k)
+                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i+1, j, k)
+                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
+                    local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
+                    do l = 1, 3
+                        ! take the cross products for the torque componenet
+                        call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                        call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                    end do
 
-                            do l = 1, 3
-                                $:GPU_ATOMIC(atomic='update')
-                                forces(ib_idx, l) = forces(ib_idx, l) - (local_force_contribution(l)*cell_volume)
-                                $:GPU_ATOMIC(atomic='update')
-                                torques(ib_idx, l) = torques(ib_idx, l) - local_torque_contribution(l)*cell_volume
-                            end do
-                        end if
+                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
+                    local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
+                    
+                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j-1, k)
+                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j+1, k)
+                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy)
+                    local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
+                    do l = 1, 3
+                        call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                        call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                    end do
+
+                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
+                    local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(2, 1:3)
+
+                    if (num_dims == 3) then
+                        call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j, k-1)
+                        call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j, k+1)
+                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
+                        local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
+                        do l = 1, 3
+                            call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                            call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                        end do
+                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
+                        local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(3, 1:3)
                     end if
+                end if
+
+                do l = 1, 3
+                    $:GPU_ATOMIC(atomic='update')
+                    forces(ib_idx, l) = forces(ib_idx, l) - (local_force_contribution(l)*cell_volume)
+                    $:GPU_ATOMIC(atomic='update')
+                    torques(ib_idx, l) = torques(ib_idx, l) - local_torque_contribution(l)*cell_volume
                 end do
-            end do
+            end if
         end do
         $:END_GPU_PARALLEL_LOOP()
 
@@ -1160,9 +1170,11 @@ contains
 
         ! if the IB is in 2D or a 3D sphere, we can compute this exactly
         if (patch_ib(ib_marker)%geometry == 2) then ! circle
-            patch_ib(ib_marker)%moment = 0.5*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2
+            patch_ib(ib_marker)%moment = 0.5_wp * patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2
         elseif (patch_ib(ib_marker)%geometry == 3) then ! rectangle
             patch_ib(ib_marker)%moment = patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)/6._wp
+        elseif (patch_ib(ib_marker)%geometry ==63) then ! ellipse
+            patch_ib(ib_marker)%moment = 0.25_wp*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)
         elseif (patch_ib(ib_marker)%geometry == 8) then ! sphere
             patch_ib(ib_marker)%moment = 0.4*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2
 
diff --git a/src/simulation/m_time_steppers.fpp b/src/simulation/m_time_steppers.fpp
index 959629cfd0..1a6b1fd18c 100644
--- a/src/simulation/m_time_steppers.fpp
+++ b/src/simulation/m_time_steppers.fpp
@@ -627,7 +627,7 @@ contains
 
                             if (patch_ib(i)%moving_ibm == 2) then ! if we are using two-way coupling, apply force and torque
                                 ! compute the force and torque on the IB from the fluid
-                                call s_compute_ib_forces(q_prim_vf, fluid_pp(1)%Re(1), fluid_pp(1)%Re(2))
+                                call s_compute_ib_forces(q_prim_vf, 1._wp / fluid_pp(1)%Re(1))
 
                                 ! update the velocity from the force value
                                 patch_ib(i)%vel = patch_ib(i)%vel + rk_coef(s, 3)*dt*(patch_ib(i)%force/patch_ib(i)%mass)/rk_coef(s, 4)
diff --git a/src/simulation/m_viscous.fpp b/src/simulation/m_viscous.fpp
index fdb201ee19..855befec84 100644
--- a/src/simulation/m_viscous.fpp
+++ b/src/simulation/m_viscous.fpp
@@ -1513,22 +1513,21 @@ contains
     end subroutine s_compute_fd_gradient
 
     ! computes the viscous stress tensor at a particule i, j, k element
-    subroutine s_compute_viscous_stress_tensor(viscous_stress_tensor, q_prim_vf, dynamic_viscosity, bulk_viscosity, i, j, k)
+    subroutine s_compute_viscous_stress_tensor(viscous_stress_tensor, q_prim_vf, dynamic_viscosity, i, j, k)
       $:GPU_ROUTINE(parallelism='[seq]')
 
       real(wp), dimension(1:3, 1:3), intent(inout) :: viscous_stress_tensor
       type(scalar_field), dimension(1:sys_size), intent(in) :: q_prim_vf
-      real(wp), intent(in) :: dynamic_viscosity, bulk_viscosity
+      real(wp), intent(in) :: dynamic_viscosity
       integer, intent(in) :: i, j, k
 
-      real(wp), dimension(1:3, 1:3) :: velocity_gradient_tensor, shear_strain_tensor
+      real(wp), dimension(1:3, 1:3) :: velocity_gradient_tensor
       real(wp), dimension(1:3) :: dx
       real(wp) :: divergence
       integer :: l, q ! iterators
 
       ! zero the viscous stress, collection of velocity diriviatives, and spacial finite differences
       viscous_stress_tensor = 0._wp
-      shear_strain_tensor = 0._wp
       velocity_gradient_tensor = 0._wp
       dx = 0._wp
 
@@ -1549,25 +1548,30 @@ contains
       end do
 
       ! compute divergence
-      divergence = velocity_gradient_tensor(1, 1) + velocity_gradient_tensor(2, 2) + velocity_gradient_tensor(3, 3)
+      divergence = 0._wp
+      do l = 1, num_dims
+          divergence = divergence + velocity_gradient_tensor(l, l)
+      end do
 
       ! set up the shear stress tensor
       do l = 1, num_dims
           do q = 1, num_dims
-              shear_strain_tensor(l, q) = 0.5_wp * (velocity_gradient_tensor(l,q) + velocity_gradient_tensor(q,l))
+              viscous_stress_tensor(l, q) = dynamic_viscosity * (velocity_gradient_tensor(l,q) + velocity_gradient_tensor(q,l))
           end do
       end do
 
       ! populate the viscous_stress_tensor
       do l = 1, num_dims
-          do q = 1, num_dims
-              viscous_stress_tensor(l, q) = shear_strain_tensor(l, q)*dynamic_viscosity*2._wp
-              if (l == q) then
-                  viscous_stress_tensor(l, q) = viscous_stress_tensor(l, q) + divergence * bulk_viscosity
-              end if
-          end do
+          viscous_stress_tensor(l, l) = viscous_stress_tensor(l, l) - 2._wp * divergence * dynamic_viscosity / 3._wp
       end do
 
+      if (num_dims == 2) then
+          do l = 1, 3
+              viscous_stress_tensor(3, l) = 0._wp
+              viscous_stress_tensor(l, 3) = 0._wp
+          end do
+      end if
+
     end subroutine s_compute_viscous_stress_tensor
 
     impure subroutine s_finalize_viscous_module()

From 989414794e778ebd5593f7339d18bcf2efd9fa54 Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Fri, 19 Dec 2025 15:40:56 -0500
Subject: [PATCH 11/34] Case file modifications

---
 examples/2D_mibm_falling_sediment/case.py | 45 ++++++++++++++---------
 1 file changed, 28 insertions(+), 17 deletions(-)

diff --git a/examples/2D_mibm_falling_sediment/case.py b/examples/2D_mibm_falling_sediment/case.py
index f61dd9293d..6726d6edd6 100644
--- a/examples/2D_mibm_falling_sediment/case.py
+++ b/examples/2D_mibm_falling_sediment/case.py
@@ -4,6 +4,11 @@
 Mu = 1.84e-05
 gam_a = 1.4
 
+total_time = 2.0
+num_time_steps = 500000
+num_saves = 200
+
+
 # Configuring case dictionary
 print(
     json.dumps(
@@ -20,13 +25,13 @@
             "y_domain%beg": 0.0e00,
             "y_domain%end": 6.0e-03,
             "cyl_coord": "F",
-            "m": 250,
-            "n": 250,
+            "m": 200,
+            "n": 800,
             "p": 0,
-            "dt": 0.5e-5,
+            "dt": float(total_time / num_time_steps),
             "t_step_start": 0,
-            "t_step_stop": 5000,  # 3000
-            "t_step_save": 50,  # 10
+            "t_step_stop": int(num_time_steps),  # 3000
+            "t_step_save": int(num_time_steps / 200),  # 10
             # Simulation Algorithm Parameters
             # Only one patches are necessary, the air tube
             "num_patches": 1,
@@ -70,11 +75,11 @@
             # Patch: Constant Tube filled with air
             # Specify the cylindrical air tube grid geometry
             "patch_icpp(1)%geometry": 3,
-            "patch_icpp(1)%x_centroid": 3.0e-03,
+            "patch_icpp(1)%x_centroid": 0.2,
             # Uniform medium density, centroid is at the center of the domain
-            "patch_icpp(1)%y_centroid": 3.0e-03,
-            "patch_icpp(1)%length_x": 6.0e-03,
-            "patch_icpp(1)%length_y": 6.0e-03,
+            "patch_icpp(1)%y_centroid": 1.4,
+            "patch_icpp(1)%length_x": 0.4,
+            "patch_icpp(1)%length_y": 2.8,
             # Specify the patch primitive variables
             "patch_icpp(1)%vel(1)": 0.00e00,
             "patch_icpp(1)%vel(2)": 0.0e00,
@@ -84,18 +89,24 @@
             # Patch: Cylinder Immersed Boundary
             "patch_ib(1)%geometry": 6,
             "patch_ib(1)%moving_ibm": 2,
-            "patch_ib(1)%x_centroid": 1.5e-03,
-            "patch_ib(1)%y_centroid": 3.0e-03,
-            "patch_ib(1)%length_x": 0.4e-03,
-            "patch_ib(1)%length_y": 0.2e-03,
-            "patch_ib(1)%vel(2)": -0.05e00,
-            "patch_ib(1)%angles(3)": -math.pi / 4.,
-            "patch_ib(1)%mass": 1.0e-6, 
+            "patch_ib(1)%x_centroid": 0.2,
+            "patch_ib(1)%y_centroid": 2.4,
+            "patch_ib(1)%length_x": 0.1,
+            "patch_ib(1)%length_y": 0.05,
+            "patch_ib(1)%vel(2)": 0.00e00,
+            "patch_ib(1)%angles(3)": math.pi / 4.,
+            "patch_ib(1)%mass": 1.1e-6, 
             "patch_ib(1)%slip": "F",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
             "fluid_pp(1)%pi_inf": 0,
-            "fluid_pp(1)%Re(1)": 2500000,
+            "fluid_pp(1)%Re(1)": 1000000,
+            # Body Forces
+            "bf_y": "T",
+            "k_y": 0.0,
+            "w_y": 0.0,
+            "p_y": 0.0,
+            "g_y": -9.81,  # gravity
         }
     )
 )

From b949d6c554c63f45d4a3349fe5d8a6bda452ce0a Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 19 Dec 2025 20:36:15 -0500
Subject: [PATCH 12/34] Found a couple errors

---
 src/simulation/m_ibm.fpp | 163 +++++++++++++++++++--------------------
 1 file changed, 81 insertions(+), 82 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 19a91b55c3..91b3449299 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1027,108 +1027,107 @@ contains
         forces = 0._wp
         torques = 0._wp
 
-        ! TODO :: Change this to a loop over ghost points
-        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
-        do gp_id = 1, num_gps
-            i = ghost_points(gp_id)%loc(1)
-            j = ghost_points(gp_id)%loc(2)
-            k = ghost_points(gp_id)%loc(3)
-            ib_idx = ghost_points(gp_id)%ib_patch_id
-            if (ib_idx /= 0 .and. patch_ib(ib_idx)%moving_ibm == 2) then ! only need to compute the gradient for cells inside a IB
-                ! get the vector pointing to the grid cell from the IB centroid
-                if (num_dims == 3) then
-                    radial_vector = [x_cc(i), y_cc(j), z_cc(k)] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, patch_ib(ib_idx)%z_centroid]
-                else
-                    radial_vector = [x_cc(i), y_cc(j), 0._wp] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, 0._wp]
-                end if
-                dx = x_cc(i + 1) - x_cc(i)
-                dy = y_cc(j + 1) - y_cc(j)
-
-                ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
-                local_force_contribution(1) = (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx)
-                local_force_contribution(2) = (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
-                cell_volume = dx*dy
-                ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
-                if (num_dims == 3) then
-                    dz = z_cc(k + 1) - z_cc(k)
-                    local_force_contribution(3) = (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
-                    cell_volume = cell_volume*dz
-                else
-                  local_force_contribution(3) = 0._wp
-                end if
-
-                ! Update the force values atomically to prevent race conditions
-                call s_cross_product(radial_vector, local_force_contribution, local_torque_contribution)
-
-                ! get the viscous stress and add its contribution if that is considered
-                ! TODO :: This is really bad code
-                ! if (viscous) then
-                if (viscous) then
-                    ! get the linear force component first
-                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i-1, j, k)
-                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i+1, j, k)
-                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
-                    local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
-                    do l = 1, 3
-                        ! take the cross products for the torque componenet
-                        call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                        call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
-                    end do
-
-                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
-                    local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
-                    
-                    call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j-1, k)
-                    call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j+1, k)
-                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy)
-                    local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
-                    do l = 1, 3
-                        call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                        call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
-                    end do
+        if (num_gps > 0) then
+            $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
+            do gp_id = 1, num_gps
+                i = ghost_points(gp_id)%loc(1)
+                j = ghost_points(gp_id)%loc(2)
+                k = ghost_points(gp_id)%loc(3)
+                ib_idx = ghost_points(gp_id)%ib_patch_id
+                if (ib_idx /= 0 .and. patch_ib(ib_idx)%moving_ibm == 2) then ! only need to compute the gradient for cells inside a IB
+                    ! get the vector pointing to the grid cell from the IB centroid
+                    if (num_dims == 3) then
+                        radial_vector = [x_cc(i), y_cc(j), z_cc(k)] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, patch_ib(ib_idx)%z_centroid]
+                    else
+                        radial_vector = [x_cc(i), y_cc(j), 0._wp] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, 0._wp]
+                    end if
+                    dx = x_cc(i + 1) - x_cc(i)
+                    dy = y_cc(j + 1) - y_cc(j)
+
+                    ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
+                    local_force_contribution(1) = (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx)
+                    local_force_contribution(2) = (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
+                    cell_volume = dx*dy
+                    ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
+                    if (num_dims == 3) then
+                        dz = z_cc(k + 1) - z_cc(k)
+                        local_force_contribution(3) = (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
+                        cell_volume = cell_volume*dz
+                    else
+                      local_force_contribution(3) = 0._wp
+                    end if
 
-                    viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
-                    local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(2, 1:3)
+                    ! Update the force values atomically to prevent race conditions
+                    call s_cross_product(radial_vector, local_force_contribution, local_torque_contribution)
+
+                    ! get the viscous stress and add its contribution if that is considered
+                    ! TODO :: This is really bad code
+                    if (viscous) then
+                        ! get the linear force component first
+                        call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i-1, j, k)
+                        call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i+1, j, k)
+                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
+                        local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
+                        do l = 1, 3
+                            ! take the cross products for the torque componenet
+                            call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                            call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                        end do
 
-                    if (num_dims == 3) then
-                        call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j, k-1)
-                        call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j, k+1)
-                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
-                        local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
+                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
+                        local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
+                        
+                        call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j-1, k)
+                        call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j+1, k)
+                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy)
+                        local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
                         do l = 1, 3
                             call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
                             call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
                         end do
-                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
-                        local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(3, 1:3)
+
+                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
+                        local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(2, 1:3)
+
+                        if (num_dims == 3) then
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j, k-1)
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j, k+1)
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
+                            local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
+                            do l = 1, 3
+                                call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                                call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                            end do
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
+                            local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(3, 1:3)
+                        end if
                     end if
-                end if
 
-                do l = 1, 3
-                    $:GPU_ATOMIC(atomic='update')
-                    forces(ib_idx, l) = forces(ib_idx, l) - (local_force_contribution(l)*cell_volume)
-                    $:GPU_ATOMIC(atomic='update')
-                    torques(ib_idx, l) = torques(ib_idx, l) - local_torque_contribution(l)*cell_volume
-                end do
-            end if
-        end do
-        $:END_GPU_PARALLEL_LOOP()
+                    do l = 1, 3
+                        $:GPU_ATOMIC(atomic='update')
+                        forces(ib_idx, l) = forces(ib_idx, l) - (local_force_contribution(l)*cell_volume)
+                        $:GPU_ATOMIC(atomic='update')
+                        torques(ib_idx, l) = torques(ib_idx, l) - local_torque_contribution(l)*cell_volume
+                    end do
+                end if
+            end do
+            $:END_GPU_PARALLEL_LOOP()
+        end if
 
         ! reduce the forces across all MPI ranks
         call s_mpi_allreduce_vectors_sum(forces, forces, num_ibs, 3)
         call s_mpi_allreduce_vectors_sum(torques, torques, num_ibs, 3)
 
         ! consider body forces after reducing to avoid double counting
-        
         do i = 1, num_ibs
           if (bf_x) then
-              forces(i, 1) = forces(i, 1) + accel_bf(1)*patch_ib(ib_idx)%mass
+              forces(i, 1) = forces(i, 1) + accel_bf(1)*patch_ib(i)%mass
           end if
           if (bf_y) then
-              forces(i, 2) = forces(i, 3) + accel_bf(2)*patch_ib(ib_idx)%mass
+              forces(i, 2) = forces(i, 2) + accel_bf(2)*patch_ib(i)%mass
           end if
           if (bf_z) then
-              forces(i, 3) = forces(i, 3) + accel_bf(3)*patch_ib(ib_idx)%mass
+              forces(i, 3) = forces(i, 3) + accel_bf(3)*patch_ib(i)%mass
           end if
         end do
 

From 02d45bd3b4d8359e9135835ccfca3fce8a2627df Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Sat, 20 Dec 2025 12:22:23 -0500
Subject: [PATCH 13/34] Updated case file

---
 examples/2D_mibm_falling_sediment/case.py | 27 +++++++++++------------
 1 file changed, 13 insertions(+), 14 deletions(-)

diff --git a/examples/2D_mibm_falling_sediment/case.py b/examples/2D_mibm_falling_sediment/case.py
index 6726d6edd6..25fd8837be 100644
--- a/examples/2D_mibm_falling_sediment/case.py
+++ b/examples/2D_mibm_falling_sediment/case.py
@@ -5,9 +5,10 @@
 gam_a = 1.4
 
 total_time = 2.0
-num_time_steps = 500000
+num_time_steps = 100000
+dt = float(total_time / num_time_steps)
 num_saves = 200
-
+steps_per_save = int(num_time_steps / num_saves)
 
 # Configuring case dictionary
 print(
@@ -18,20 +19,18 @@
             # Computational Domain Parameters
             # For these computations, the cylinder is placed at the (0,0,0)
             # domain origin.
-            # axial direction
-            "x_domain%beg": 0.0e00,
-            "x_domain%end": 6.0e-03,
-            # r direction
-            "y_domain%beg": 0.0e00,
-            "y_domain%end": 6.0e-03,
+            "x_domain%beg": 0.0,
+            "x_domain%end": 0.4,
+            "y_domain%beg": 0.0,
+            "y_domain%end": 2.8,
             "cyl_coord": "F",
-            "m": 200,
-            "n": 800,
+            "m": 100,
+            "n": 700,
             "p": 0,
-            "dt": float(total_time / num_time_steps),
+            "dt": dt,
             "t_step_start": 0,
-            "t_step_stop": int(num_time_steps),  # 3000
-            "t_step_save": int(num_time_steps / 200),  # 10
+            "t_step_stop": num_time_steps,  # 3000
+            "t_step_save": steps_per_save,  # 10
             # Simulation Algorithm Parameters
             # Only one patches are necessary, the air tube
             "num_patches": 1,
@@ -100,7 +99,7 @@
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
             "fluid_pp(1)%pi_inf": 0,
-            "fluid_pp(1)%Re(1)": 1000000,
+            "fluid_pp(1)%Re(1)": 100000,
             # Body Forces
             "bf_y": "T",
             "k_y": 0.0,

From 61e33089912b95f7d001d7826eecd276c069fc87 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Mon, 22 Dec 2025 13:44:07 -0500
Subject: [PATCH 14/34] Fixed the IB errors

---
 src/simulation/m_ibm.fpp | 164 ++++++++++++++++++++-------------------
 1 file changed, 85 insertions(+), 79 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 91b3449299..231cf17f42 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -212,8 +212,10 @@ contains
                                   rho = rho + q_prim_vf(contxb+i-1)%sf(j, k, l)
                               end do
 
+                              ! Sets thhe momentum
                               do i = 1, num_dims
                                   q_cons_vf(momxb+i-1)%sf(j, k, l) = patch_ib(patch_id)%vel(i) * rho
+                                  q_prim_vf(momxb+i-1)%sf(j, k, l) = patch_ib(patch_id)%vel(i)
                               end do
                         end if
                     end if
@@ -1021,98 +1023,98 @@ contains
         integer :: gp_id, i, j, k, l, q, ib_idx
         real(wp), dimension(num_ibs, 3) :: forces, torques
         real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2 ! viscous stress tensor with temp vectors to hold divergence calculations 
-        real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution
+        real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution, vel
         real(wp) :: cell_volume, dx, dy, dz
 
         forces = 0._wp
         torques = 0._wp
 
-        if (num_gps > 0) then
-            $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
-            do gp_id = 1, num_gps
-                i = ghost_points(gp_id)%loc(1)
-                j = ghost_points(gp_id)%loc(2)
-                k = ghost_points(gp_id)%loc(3)
-                ib_idx = ghost_points(gp_id)%ib_patch_id
-                if (ib_idx /= 0 .and. patch_ib(ib_idx)%moving_ibm == 2) then ! only need to compute the gradient for cells inside a IB
-                    ! get the vector pointing to the grid cell from the IB centroid
-                    if (num_dims == 3) then
-                        radial_vector = [x_cc(i), y_cc(j), z_cc(k)] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, patch_ib(ib_idx)%z_centroid]
-                    else
-                        radial_vector = [x_cc(i), y_cc(j), 0._wp] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, 0._wp]
-                    end if
-                    dx = x_cc(i + 1) - x_cc(i)
-                    dy = y_cc(j + 1) - y_cc(j)
-
-                    ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
-                    local_force_contribution(1) = (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx)
-                    local_force_contribution(2) = (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
-                    cell_volume = dx*dy
-                    ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
-                    if (num_dims == 3) then
-                        dz = z_cc(k + 1) - z_cc(k)
-                        local_force_contribution(3) = (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
-                        cell_volume = cell_volume*dz
-                    else
-                      local_force_contribution(3) = 0._wp
-                    end if
-
-                    ! Update the force values atomically to prevent race conditions
-                    call s_cross_product(radial_vector, local_force_contribution, local_torque_contribution)
-
-                    ! get the viscous stress and add its contribution if that is considered
-                    ! TODO :: This is really bad code
-                    if (viscous) then
-                        ! get the linear force component first
-                        call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i-1, j, k)
-                        call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i+1, j, k)
-                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
-                        local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
-                        do l = 1, 3
-                            ! take the cross products for the torque componenet
-                            call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                            call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
-                        end do
-
-                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
-                        local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
-                        
-                        call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j-1, k)
-                        call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j+1, k)
-                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy)
-                        local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
-                        do l = 1, 3
-                            call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                            call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
-                        end do
+        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
+        do i = 0, m
+            do j = 0, n
+                do k = 0, p
+                    ib_idx = ib_markers%sf(i, j, k)
+                    if (ib_idx /= 0) then
+                        ! get the vector pointing to the grid cell from the IB centroid
+                        if (num_dims == 3) then
+                            radial_vector = [x_cc(i), y_cc(j), z_cc(k)] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, patch_ib(ib_idx)%z_centroid]
+                        else
+                            radial_vector = [x_cc(i), y_cc(j), 0._wp] - [patch_ib(ib_idx)%x_centroid, patch_ib(ib_idx)%y_centroid, 0._wp]
+                        end if
+                        dx = x_cc(i + 1) - x_cc(i)
+                        dy = y_cc(j + 1) - y_cc(j)
+
+                        ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
+                        local_force_contribution(1) = -1._wp * (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx) ! force is the negative pressure gradient
+                        local_force_contribution(2) = -1._wp * (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
+                        cell_volume = abs(dx*dy)
+                        ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
+                        if (num_dims == 3) then
+                            dz = z_cc(k + 1) - z_cc(k)
+                            local_force_contribution(3) = -1._wp * (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
+                            cell_volume = abs(cell_volume*dz)
+                        else
+                          local_force_contribution(3) = 0._wp
+                        end if
 
-                        viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
-                        local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(2, 1:3)
+                        ! Update the force values atomically to prevent race conditions
+                        call s_cross_product(radial_vector, local_force_contribution, local_torque_contribution)
+
+                        ! get the viscous stress and add its contribution if that is considered
+                        ! TODO :: This is really bad code
+                        ! if (.false.) then
+                        if (viscous) then
+                            ! get the linear force component first
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i-1, j, k)
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i+1, j, k)
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
+                            local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
+                            do l = 1, 3
+                                ! take the cross products for the torque componenet
+                                call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                                call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                            end do
 
-                        if (num_dims == 3) then
-                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j, k-1)
-                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j, k+1)
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
-                            local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
+                            local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
+                            
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j-1, k)
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j+1, k)
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy)
+                            local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
                             do l = 1, 3
                                 call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
                                 call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
                             end do
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
-                            local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(3, 1:3)
+
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
+                            local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(2, 1:3)
+
+                            if (num_dims == 3) then
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j, k-1)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j, k+1)
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
+                                local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
+                                do l = 1, 3
+                                    call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
+                                    call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                                end do
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
+                                local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(3, 1:3)
+                            end if
                         end if
-                    end if
 
-                    do l = 1, 3
-                        $:GPU_ATOMIC(atomic='update')
-                        forces(ib_idx, l) = forces(ib_idx, l) - (local_force_contribution(l)*cell_volume)
-                        $:GPU_ATOMIC(atomic='update')
-                        torques(ib_idx, l) = torques(ib_idx, l) - local_torque_contribution(l)*cell_volume
-                    end do
-                end if
+                        do l = 1, 3
+                            $:GPU_ATOMIC(atomic='update')
+                            forces(ib_idx, l) = forces(ib_idx, l) + (local_force_contribution(l)*cell_volume)
+                            $:GPU_ATOMIC(atomic='update')
+                            torques(ib_idx, l) = torques(ib_idx, l) + local_torque_contribution(l)*cell_volume
+                        end do
+                    end if
+                end do
             end do
-            $:END_GPU_PARALLEL_LOOP()
-        end if
+        end do
+        $:END_GPU_PARALLEL_LOOP()
 
         ! reduce the forces across all MPI ranks
         call s_mpi_allreduce_vectors_sum(forces, forces, num_ibs, 3)
@@ -1137,6 +1139,10 @@ contains
             patch_ib(i)%torque(:) = matmul(patch_ib(i)%rotation_matrix_inverse, torques(i, :)) ! torques must be computed in the local coordinates of the IB
         end do
 
+        ! print *, "drag force: ", forces(1, 1:2), " || torque: ", torques(1, 3)
+        vel = [0.05_wp, 0._wp, 0._wp] - patch_ib(1)%vel
+        print *, "drag coef: ", 2._wp * sqrt(dot_product(forces(1, :), forces(1, :))) / ((sqrt(dot_product(vel,vel))**2) * 2._wp * 0.3e-03)
+
     end subroutine s_compute_ib_forces
 
     !> Subroutine to deallocate memory reserved for the IBM module
@@ -1172,7 +1178,7 @@ contains
             patch_ib(ib_marker)%moment = 0.5_wp * patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2
         elseif (patch_ib(ib_marker)%geometry == 3) then ! rectangle
             patch_ib(ib_marker)%moment = patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)/6._wp
-        elseif (patch_ib(ib_marker)%geometry ==63) then ! ellipse
+        elseif (patch_ib(ib_marker)%geometry == 6) then ! ellipse
             patch_ib(ib_marker)%moment = 0.25_wp*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)
         elseif (patch_ib(ib_marker)%geometry == 8) then ! sphere
             patch_ib(ib_marker)%moment = 0.4*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2

From aa5c0e48cc80d428cff78808539061b29bbeb9e1 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Mon, 22 Dec 2025 15:49:16 -0500
Subject: [PATCH 15/34] Fixed torque not actually applying a rotation and
 randomly causing nans

---
 src/simulation/m_ibm.fpp | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 231cf17f42..1dd25d564e 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -98,8 +98,8 @@ contains
         moving_immersed_boundary_flag = .false.
         do i = 1, num_ibs
             if (patch_ib(i)%moving_ibm /= 0) then
+              call s_compute_moment_of_inertia(i, patch_ib(i)%angular_vel)
                 moving_immersed_boundary_flag = .true.
-
             end if
             call s_update_ib_rotation_matrix(i)
         end do
@@ -1139,9 +1139,9 @@ contains
             patch_ib(i)%torque(:) = matmul(patch_ib(i)%rotation_matrix_inverse, torques(i, :)) ! torques must be computed in the local coordinates of the IB
         end do
 
-        ! print *, "drag force: ", forces(1, 1:2), " || torque: ", torques(1, 3)
-        vel = [0.05_wp, 0._wp, 0._wp] - patch_ib(1)%vel
-        print *, "drag coef: ", 2._wp * sqrt(dot_product(forces(1, :), forces(1, :))) / ((sqrt(dot_product(vel,vel))**2) * 2._wp * 0.3e-03)
+        ! print *, "Acceleration: ", forces(1, 1:2) / patch_ib(1)%mass, " || torque: ", torques(1, 3)
+        ! vel = [0.05_wp, 0._wp, 0._wp] - patch_ib(1)%vel
+        ! print *, "drag coef: ", 2._wp * sqrt(dot_product(forces(1, :), forces(1, :))) / (dot_product(vel,vel) * 2._wp * 0.3e-03)
 
     end subroutine s_compute_ib_forces
 
@@ -1156,21 +1156,21 @@ contains
 
     subroutine s_compute_moment_of_inertia(ib_marker, axis)
 
-        real(wp), dimension(3), optional :: axis !< the axis about which we compute the moment. Only required in 3D.
+        real(wp), dimension(3), intent(in) :: axis !< the axis about which we compute the moment. Only required in 3D.
         integer, intent(in) :: ib_marker
 
         real(wp) :: moment, distance_to_axis, cell_volume
-        real(wp), dimension(3) :: position, closest_point_along_axis, vector_to_axis
+        real(wp), dimension(3) :: position, closest_point_along_axis, vector_to_axis, normal_axis
         integer :: i, j, k, count
 
         if (p == 0) then
-            axis = [0, 1, 0]
+            normal_axis = [0, 1, 0]
         else if (sqrt(sum(axis**2)) == 0) then
             ! if the object is not actually rotating at this time, return a dummy value and exit
             patch_ib(ib_marker)%moment = 1._wp
             return
         else
-            axis = axis/sqrt(sum(axis))
+            normal_axis = axis/sqrt(sum(axis))
         end if
 
         ! if the IB is in 2D or a 3D sphere, we can compute this exactly
@@ -1191,7 +1191,7 @@ contains
                 cell_volume = cell_volume*(z_cc(1) - z_cc(0))
             end if
 
-            $:GPU_PARALLEL_LOOP(private='[position,closest_point_along_axis,vector_to_axis,distance_to_axis]', copy='[moment,count]', copyin='[ib_marker,cell_volume,axis]', collapse=3)
+            $:GPU_PARALLEL_LOOP(private='[position,closest_point_along_axis,vector_to_axis,distance_to_axis]', copy='[moment,count]', copyin='[ib_marker,cell_volume,normal_axis]', collapse=3)
             do i = 0, m
                 do j = 0, n
                     do k = 0, p
@@ -1207,7 +1207,7 @@ contains
                             end if
 
                             ! project the position along the axis to find the closest distance to the rotation axis
-                            closest_point_along_axis = axis*dot_product(axis, position)
+                            closest_point_along_axis = normal_axis*dot_product(axis, position)
                             vector_to_axis = position - closest_point_along_axis
                             distance_to_axis = dot_product(vector_to_axis, vector_to_axis) ! saves the distance to the axis squared
 

From 1a5a903c24fdceeb104439490df2c3b24cefd0b2 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Tue, 23 Dec 2025 13:47:34 -0500
Subject: [PATCH 16/34] Changes to the falling sediment that make it more
 in-line with the original paper

---
 examples/2D_mibm_falling_sediment/case.py | 44 ++++++++++++-----------
 1 file changed, 23 insertions(+), 21 deletions(-)

diff --git a/examples/2D_mibm_falling_sediment/case.py b/examples/2D_mibm_falling_sediment/case.py
index 25fd8837be..efd7a04162 100644
--- a/examples/2D_mibm_falling_sediment/case.py
+++ b/examples/2D_mibm_falling_sediment/case.py
@@ -7,9 +7,11 @@
 total_time = 2.0
 num_time_steps = 100000
 dt = float(total_time / num_time_steps)
-num_saves = 200
+num_saves = 1000
 steps_per_save = int(num_time_steps / num_saves)
 
+length = 0.4e-2
+
 # Configuring case dictionary
 print(
     json.dumps(
@@ -19,10 +21,10 @@
             # Computational Domain Parameters
             # For these computations, the cylinder is placed at the (0,0,0)
             # domain origin.
-            "x_domain%beg": 0.0,
-            "x_domain%end": 0.4,
-            "y_domain%beg": 0.0,
-            "y_domain%end": 2.8,
+            "x_domain%beg": 0.0e-2,
+            "x_domain%end": length,
+            "y_domain%beg": 0.0e-2,
+            "y_domain%end": 7.*length,
             "cyl_coord": "F",
             "m": 100,
             "n": 700,
@@ -57,10 +59,10 @@
             "riemann_solver": 2,
             "wave_speeds": 1,
             # We use ghost-cell
-            "bc_x%beg": -3,
-            "bc_x%end": -3,
-            "bc_y%beg": -3,
-            "bc_y%end": -3,
+            "bc_x%beg": -15,
+            "bc_x%end": -15,
+            "bc_y%beg": -15,
+            "bc_y%end": -15,
             # Set IB to True and add 1 patch
             "ib": "T",
             "num_ibs": 1,
@@ -74,32 +76,32 @@
             # Patch: Constant Tube filled with air
             # Specify the cylindrical air tube grid geometry
             "patch_icpp(1)%geometry": 3,
-            "patch_icpp(1)%x_centroid": 0.2,
+            "patch_icpp(1)%x_centroid": length/2.,
             # Uniform medium density, centroid is at the center of the domain
-            "patch_icpp(1)%y_centroid": 1.4,
-            "patch_icpp(1)%length_x": 0.4,
-            "patch_icpp(1)%length_y": 2.8,
+            "patch_icpp(1)%y_centroid": 7.*length/2.,
+            "patch_icpp(1)%length_x": length,
+            "patch_icpp(1)%length_y": 7. * length,
             # Specify the patch primitive variables
             "patch_icpp(1)%vel(1)": 0.00e00,
             "patch_icpp(1)%vel(2)": 0.0e00,
-            "patch_icpp(1)%pres": 1.0e00,
+            "patch_icpp(1)%pres": f"1.0 + 9.81*{7. * length} - 9.81*y", # Set up a linear pressure gradient to start with # 1.0e00 at the top,
             "patch_icpp(1)%alpha_rho(1)": 1.0e00,
             "patch_icpp(1)%alpha(1)": 1.0e00,
             # Patch: Cylinder Immersed Boundary
             "patch_ib(1)%geometry": 6,
             "patch_ib(1)%moving_ibm": 2,
-            "patch_ib(1)%x_centroid": 0.2,
-            "patch_ib(1)%y_centroid": 2.4,
-            "patch_ib(1)%length_x": 0.1,
-            "patch_ib(1)%length_y": 0.05,
-            "patch_ib(1)%vel(2)": 0.00e00,
+            "patch_ib(1)%x_centroid": length/2.,
+            "patch_ib(1)%y_centroid": 6. * length,
+            "patch_ib(1)%length_x": length / 4.,
+            "patch_ib(1)%length_y": length / 8,
+            "patch_ib(1)%vel(2)": 0.0e00,
             "patch_ib(1)%angles(3)": math.pi / 4.,
-            "patch_ib(1)%mass": 1.1e-6, 
+            "patch_ib(1)%mass": 1.1 * math.pi * length * length / 32., # density of 1.1e-6 times the volume of the ellipse
             "patch_ib(1)%slip": "F",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
             "fluid_pp(1)%pi_inf": 0,
-            "fluid_pp(1)%Re(1)": 100000,
+            "fluid_pp(1)%Re(1)": 100000, # kenimatic viscosity of 0.01 cm^2/s
             # Body Forces
             "bf_y": "T",
             "k_y": 0.0,

From 4c2b02d68dbb19f5a66993d664f921df804ae343 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Wed, 24 Dec 2025 11:08:03 -0500
Subject: [PATCH 17/34] Minor clean ups

---
 examples/2D_mibm_falling_sediment/case.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/examples/2D_mibm_falling_sediment/case.py b/examples/2D_mibm_falling_sediment/case.py
index efd7a04162..8af8181e51 100644
--- a/examples/2D_mibm_falling_sediment/case.py
+++ b/examples/2D_mibm_falling_sediment/case.py
@@ -1,16 +1,18 @@
 import json
 import math
 
-Mu = 1.84e-05
+Mu = 0.1 * 1e-4 # kenimatic viscosity of 0.01 cm^2/s
 gam_a = 1.4
 
-total_time = 2.0
+total_time = 0.35
+# total_time = 2.0
 num_time_steps = 100000
 dt = float(total_time / num_time_steps)
 num_saves = 1000
 steps_per_save = int(num_time_steps / num_saves)
 
 length = 0.4e-2
+avg_speed = 5.5*length / total_time
 
 # Configuring case dictionary
 print(
@@ -101,7 +103,7 @@
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
             "fluid_pp(1)%pi_inf": 0,
-            "fluid_pp(1)%Re(1)": 100000, # kenimatic viscosity of 0.01 cm^2/s
+            "fluid_pp(1)%Re(1)": 1. / Mu,
             # Body Forces
             "bf_y": "T",
             "k_y": 0.0,

From 19808acc3615f2056313345fdcd67d5c8b8bf068 Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Mon, 5 Jan 2026 09:44:59 -0500
Subject: [PATCH 18/34] Found a factor of 4 error in the mass calculations

---
 examples/2D_mibm_falling_sediment/case.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/examples/2D_mibm_falling_sediment/case.py b/examples/2D_mibm_falling_sediment/case.py
index 8af8181e51..5361732841 100644
--- a/examples/2D_mibm_falling_sediment/case.py
+++ b/examples/2D_mibm_falling_sediment/case.py
@@ -1,7 +1,7 @@
 import json
 import math
 
-Mu = 0.1 * 1e-4 # kenimatic viscosity of 0.01 cm^2/s
+Mu = 0.01 * 1e-4 # kenimatic viscosity of 0.01 cm^2/s
 gam_a = 1.4
 
 total_time = 0.35
@@ -75,8 +75,7 @@
             "prim_vars_wrt": "T",
             "E_wrt": "T",
             "parallel_io": "T",
-            # Patch: Constant Tube filled with air
-            # Specify the cylindrical air tube grid geometry
+            # Specify the rectangle patch geometry
             "patch_icpp(1)%geometry": 3,
             "patch_icpp(1)%x_centroid": length/2.,
             # Uniform medium density, centroid is at the center of the domain
@@ -98,7 +97,7 @@
             "patch_ib(1)%length_y": length / 8,
             "patch_ib(1)%vel(2)": 0.0e00,
             "patch_ib(1)%angles(3)": math.pi / 4.,
-            "patch_ib(1)%mass": 1.1 * math.pi * length * length / 32., # density of 1.1e-6 times the volume of the ellipse
+            "patch_ib(1)%mass": 1.1 * math.pi * length * length / 128., # density of 1.1 times the volume of the ellipse to give density ratio of 1.1
             "patch_ib(1)%slip": "F",
             # Fluids Physical Parameters
             "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)

From 9f3cb404a61cc9d44ff8f95e457acbea8b889f79 Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Mon, 5 Jan 2026 15:12:49 -0500
Subject: [PATCH 19/34] corrected calculations for patches

---
 src/simulation/m_ibm.fpp | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 1dd25d564e..fb44b633f0 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1136,13 +1136,9 @@ contains
         ! apply the summed forces
         do i = 1, num_ibs
             patch_ib(i)%force(:) = forces(i, :)
-            patch_ib(i)%torque(:) = matmul(patch_ib(i)%rotation_matrix_inverse, torques(i, :)) ! torques must be computed in the local coordinates of the IB
+            patch_ib(i)%torque(:) = matmul(patch_ib(i)%rotation_matrix_inverse, torques(i, :)) ! torques must be converted to the local coordinates of the IB
         end do
 
-        ! print *, "Acceleration: ", forces(1, 1:2) / patch_ib(1)%mass, " || torque: ", torques(1, 3)
-        ! vel = [0.05_wp, 0._wp, 0._wp] - patch_ib(1)%vel
-        ! print *, "drag coef: ", 2._wp * sqrt(dot_product(forces(1, :), forces(1, :))) / (dot_product(vel,vel) * 2._wp * 0.3e-03)
-
     end subroutine s_compute_ib_forces
 
     !> Subroutine to deallocate memory reserved for the IBM module
@@ -1179,7 +1175,7 @@ contains
         elseif (patch_ib(ib_marker)%geometry == 3) then ! rectangle
             patch_ib(ib_marker)%moment = patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)/6._wp
         elseif (patch_ib(ib_marker)%geometry == 6) then ! ellipse
-            patch_ib(ib_marker)%moment = 0.25_wp*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)
+            patch_ib(ib_marker)%moment = 0.0625_wp*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)
         elseif (patch_ib(ib_marker)%geometry == 8) then ! sphere
             patch_ib(ib_marker)%moment = 0.4*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2
 

From 9ffed4e587a09508c8ef896a5729de463eaec855 Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 11:22:10 -0500
Subject: [PATCH 20/34] removed falling sediment, as it is a bad comparison,
 but replaced it with a shock cylinder

---
 examples/2D_mibm_falling_sediment/case.py | 114 ------------------
 examples/2D_mibm_shock_cylinder/case.py   | 136 ++++++++++++++++++++++
 2 files changed, 136 insertions(+), 114 deletions(-)
 delete mode 100644 examples/2D_mibm_falling_sediment/case.py
 create mode 100644 examples/2D_mibm_shock_cylinder/case.py

diff --git a/examples/2D_mibm_falling_sediment/case.py b/examples/2D_mibm_falling_sediment/case.py
deleted file mode 100644
index 5361732841..0000000000
--- a/examples/2D_mibm_falling_sediment/case.py
+++ /dev/null
@@ -1,114 +0,0 @@
-import json
-import math
-
-Mu = 0.01 * 1e-4 # kenimatic viscosity of 0.01 cm^2/s
-gam_a = 1.4
-
-total_time = 0.35
-# total_time = 2.0
-num_time_steps = 100000
-dt = float(total_time / num_time_steps)
-num_saves = 1000
-steps_per_save = int(num_time_steps / num_saves)
-
-length = 0.4e-2
-avg_speed = 5.5*length / total_time
-
-# Configuring case dictionary
-print(
-    json.dumps(
-        {
-            # Logistics
-            "run_time_info": "T",
-            # Computational Domain Parameters
-            # For these computations, the cylinder is placed at the (0,0,0)
-            # domain origin.
-            "x_domain%beg": 0.0e-2,
-            "x_domain%end": length,
-            "y_domain%beg": 0.0e-2,
-            "y_domain%end": 7.*length,
-            "cyl_coord": "F",
-            "m": 100,
-            "n": 700,
-            "p": 0,
-            "dt": dt,
-            "t_step_start": 0,
-            "t_step_stop": num_time_steps,  # 3000
-            "t_step_save": steps_per_save,  # 10
-            # Simulation Algorithm Parameters
-            # Only one patches are necessary, the air tube
-            "num_patches": 1,
-            # Use the 5 equation model
-            "model_eqns": 2,
-            "alt_soundspeed": "F",
-            # One fluids: air
-            "num_fluids": 1,
-            # time step
-            "mpp_lim": "F",
-            # Correct errors when computing speed of sound
-            "mixture_err": "T",
-            # Use TVD RK3 for time marching
-            "time_stepper": 3,
-            # Use WENO5
-            "weno_order": 5,
-            "weno_eps": 1.0e-16,
-            "weno_Re_flux": "T",
-            "weno_avg": "T",
-            "avg_state": 2,
-            "mapped_weno": "T",
-            "null_weights": "F",
-            "mp_weno": "T",
-            "riemann_solver": 2,
-            "wave_speeds": 1,
-            # We use ghost-cell
-            "bc_x%beg": -15,
-            "bc_x%end": -15,
-            "bc_y%beg": -15,
-            "bc_y%end": -15,
-            # Set IB to True and add 1 patch
-            "ib": "T",
-            "num_ibs": 1,
-            "viscous": "T",
-            # Formatted Database Files Structure Parameters
-            "format": 1,
-            "precision": 2,
-            "prim_vars_wrt": "T",
-            "E_wrt": "T",
-            "parallel_io": "T",
-            # Specify the rectangle patch geometry
-            "patch_icpp(1)%geometry": 3,
-            "patch_icpp(1)%x_centroid": length/2.,
-            # Uniform medium density, centroid is at the center of the domain
-            "patch_icpp(1)%y_centroid": 7.*length/2.,
-            "patch_icpp(1)%length_x": length,
-            "patch_icpp(1)%length_y": 7. * length,
-            # Specify the patch primitive variables
-            "patch_icpp(1)%vel(1)": 0.00e00,
-            "patch_icpp(1)%vel(2)": 0.0e00,
-            "patch_icpp(1)%pres": f"1.0 + 9.81*{7. * length} - 9.81*y", # Set up a linear pressure gradient to start with # 1.0e00 at the top,
-            "patch_icpp(1)%alpha_rho(1)": 1.0e00,
-            "patch_icpp(1)%alpha(1)": 1.0e00,
-            # Patch: Cylinder Immersed Boundary
-            "patch_ib(1)%geometry": 6,
-            "patch_ib(1)%moving_ibm": 2,
-            "patch_ib(1)%x_centroid": length/2.,
-            "patch_ib(1)%y_centroid": 6. * length,
-            "patch_ib(1)%length_x": length / 4.,
-            "patch_ib(1)%length_y": length / 8,
-            "patch_ib(1)%vel(2)": 0.0e00,
-            "patch_ib(1)%angles(3)": math.pi / 4.,
-            "patch_ib(1)%mass": 1.1 * math.pi * length * length / 128., # density of 1.1 times the volume of the ellipse to give density ratio of 1.1
-            "patch_ib(1)%slip": "F",
-            # Fluids Physical Parameters
-            "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
-            "fluid_pp(1)%pi_inf": 0,
-            "fluid_pp(1)%Re(1)": 1. / Mu,
-            # Body Forces
-            "bf_y": "T",
-            "k_y": 0.0,
-            "w_y": 0.0,
-            "p_y": 0.0,
-            "g_y": -9.81,  # gravity
-        }
-    )
-)
diff --git a/examples/2D_mibm_shock_cylinder/case.py b/examples/2D_mibm_shock_cylinder/case.py
new file mode 100644
index 0000000000..89a2b493ce
--- /dev/null
+++ b/examples/2D_mibm_shock_cylinder/case.py
@@ -0,0 +1,136 @@
+import json
+import math
+
+# fluid parameters
+Mu = 1.84e-05
+gam_a = 1.4
+
+# domain size and speed
+mach_number = 1.5
+pre_shock_pressure = 1
+pre_shock_density = 1.4
+pre_shock_speed = 0.0
+post_shock_pressure = 2.4583
+post_shock_density = 2.6069
+post_shock_speed = 0.6944
+
+domain_size = 4.
+wave_front = -1.5
+
+total_time = 1.5
+num_time_steps = 2000
+dt = float(total_time / num_time_steps)
+num_saves = 100
+steps_to_save = int(num_time_steps / num_saves)
+
+# Configuring case dictionary
+print(
+    json.dumps(
+        {
+            # Logistics
+            "run_time_info": "T",
+            # Computational Domain Parameters
+            # For these computations, the cylinder is placed at the (0,0,0)
+            # domain origin.
+            # axial direction
+            "x_domain%beg": -domain_size * 0.5,
+            "x_domain%end": domain_size * 0.5,
+            # r direction
+            "y_domain%beg": -domain_size * 0.5,
+            "y_domain%end": domain_size * 0.5,
+            "cyl_coord": "F",
+            "m": 1000,
+            "n": 1000,
+            "p": 0,
+            "dt": dt,
+            "t_step_start": 0,
+            "t_step_stop": num_time_steps,  # 10000,
+            "t_step_save": steps_to_save,
+            # Simulation Algorithm Parameters
+            # Only one patches are necessary, the air tube
+            "num_patches": 2,
+            # Use the 5 equation model
+            "model_eqns": 2,
+            "alt_soundspeed": "F",
+            # One fluids: air
+            "num_fluids": 1,
+            # time step
+            "mpp_lim": "F",
+            # Correct errors when computing speed of sound
+            "mixture_err": "T",
+            # Use TVD RK3 for time marching
+            "time_stepper": 3,
+            # Use WENO5
+            "weno_order": 5,
+            "weno_eps": 1.0e-16,
+            "weno_Re_flux": "T",
+            "weno_avg": "T",
+            "avg_state": 2,
+            "mapped_weno": "T",
+            "null_weights": "F",
+            "mp_weno": "T",
+            "riemann_solver": 2,
+            "wave_speeds": 1,
+            # We use ghost-cell
+            "bc_x%beg": -17,
+            "bc_x%end": -8,
+            "bc_y%beg": -15,
+            "bc_y%end": -15,
+            # Set IB to True and add 1 patch
+            "ib": "T",
+            "num_ibs": 1,
+            "viscous": "T",
+            # Formatted Database Files Structure Parameters
+            "format": 1,
+            "precision": 2,
+            "prim_vars_wrt": "T",
+            "E_wrt": "T",
+            "parallel_io": "T",
+            # Patch: Constant Tube filled with air
+            # Specify the cylindrical air tube grid geometry
+            "patch_icpp(1)%geometry": 3,            
+            "patch_icpp(2)%geometry": 3,
+            # patch locations      
+            "patch_icpp(1)%x_centroid": 0.5 * wave_front + 0.25 * domain_size,
+            "patch_icpp(1)%y_centroid": 0.,
+            "patch_icpp(1)%length_x": 0.5 * domain_size - wave_front,
+            "patch_icpp(1)%length_y": domain_size,
+            "patch_icpp(2)%x_centroid": 0.5 * wave_front - 0.25 * domain_size,
+            "patch_icpp(2)%y_centroid": 0.,
+            "patch_icpp(2)%length_x": 0.5 * domain_size + wave_front,
+            "patch_icpp(2)%length_y": domain_size,
+            # Specify the patch primitive variables
+            "patch_icpp(1)%vel(1)": pre_shock_speed,
+            "patch_icpp(1)%vel(2)": 0.0,
+            "patch_icpp(1)%pres": pre_shock_pressure,
+            "patch_icpp(1)%alpha_rho(1)":  pre_shock_density,
+            "patch_icpp(1)%alpha(1)": 1.0e00,
+            "patch_icpp(2)%vel(1)": post_shock_speed,
+            "patch_icpp(2)%vel(2)": 0.0,
+            "patch_icpp(2)%pres": post_shock_pressure,
+            "patch_icpp(2)%alpha_rho(1)":  post_shock_density,
+            "patch_icpp(2)%alpha(1)": 1.0e00,
+            # Patch: Cylinder Immersed Boundary
+            "patch_ib(1)%geometry": 2,
+            "patch_ib(1)%x_centroid": -0.5,
+            "patch_ib(1)%y_centroid": 0.,
+            "patch_ib(1)%radius": 0.5,
+            "patch_ib(1)%slip": "T",
+            "patch_ib(1)%moving_ibm": 2,
+            "patch_ib(1)%vel(1)": 0,
+            "patch_ib(1)%vel(2)": 0,
+            "patch_ib(1)%vel(3)": 0,
+            "patch_ib(1)%angles(1)": 0.0,  # x-axis rotation in radians
+            "patch_ib(1)%angles(2)": 0.0,  # y-axis rotation
+            "patch_ib(1)%angles(3)": 0.0,  # z-axis rotation
+            "patch_ib(1)%angular_vel(1)": 0.0,  # x-axis rotational velocity in radians per second
+            "patch_ib(1)%angular_vel(2)": 0.0,  # y-axis rotation
+            "patch_ib(1)%angular_vel(3)": 0.0,  # z-axis rotation
+            "patch_ib(1)%mass": 0.5,  # z-axis rotation
+            # Fluids Physical Parameters
+            "fluid_pp(1)%gamma": 1.0e00 / (gam_a - 1.0e00),  # 2.50(Not 1.40)
+            "fluid_pp(1)%pi_inf": 0,
+            "fluid_pp(1)%Re(1)": 2500000,
+        }
+    )
+)

From 091a750d9a78831b9cff2469fd8810b77a053f01 Mon Sep 17 00:00:00 2001
From: "Daniel J. Vickers" <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 11:24:39 -0500
Subject: [PATCH 21/34] Added note on reference that it is from

---
 examples/2D_mibm_shock_cylinder/case.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/examples/2D_mibm_shock_cylinder/case.py b/examples/2D_mibm_shock_cylinder/case.py
index 89a2b493ce..b962b0c269 100644
--- a/examples/2D_mibm_shock_cylinder/case.py
+++ b/examples/2D_mibm_shock_cylinder/case.py
@@ -1,8 +1,10 @@
 import json
 import math
 
+# This case is a recreation of the case from "Moving overlapping grids with adaptive mesh refinement for high-speed reactive and non-reactive flow"
+# by William D. Henshaw and Donald W. Schwendeman 
+
 # fluid parameters
-Mu = 1.84e-05
 gam_a = 1.4
 
 # domain size and speed

From 18b7dcc7ad3a66260613dd23a226cb2e258257d4 Mon Sep 17 00:00:00 2001
From: Daniel J Vickers <dvickers6@atl1-1-02-007-21-2.pace.gatech.edu>
Date: Fri, 9 Jan 2026 16:12:31 -0500
Subject: [PATCH 22/34] Succesfully ran on phoenix on GPU

---
 src/simulation/m_ibm.fpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index fb44b633f0..6105a43b3f 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1029,7 +1029,7 @@ contains
         forces = 0._wp
         torques = 0._wp
 
-        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity,bulk_viscosity]', collapse=3)
+        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity]', collapse=3)
         do i = 0, m
             do j = 0, n
                 do k = 0, p

From feedba22e323e221a9a1a206719a5a3ba13977c2 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 16:27:59 -0500
Subject: [PATCH 23/34] Generated golden files

---
 tests/5600D63B/golden-metadata.txt | 193 +++++++++++++++++++++++++++++
 tests/5600D63B/golden.txt          |  11 ++
 tests/7FA04E95/golden-metadata.txt | 193 +++++++++++++++++++++++++++++
 tests/7FA04E95/golden.txt          |  11 ++
 4 files changed, 408 insertions(+)
 create mode 100644 tests/5600D63B/golden-metadata.txt
 create mode 100644 tests/5600D63B/golden.txt
 create mode 100644 tests/7FA04E95/golden-metadata.txt
 create mode 100644 tests/7FA04E95/golden.txt

diff --git a/tests/5600D63B/golden-metadata.txt b/tests/5600D63B/golden-metadata.txt
new file mode 100644
index 0000000000..87feb7fece
--- /dev/null
+++ b/tests/5600D63B/golden-metadata.txt
@@ -0,0 +1,193 @@
+This file was created on 2026-01-09 16:23:05.537791.
+
+mfc.sh:
+
+    Invocation: test --generate -o 5600D63B
+    Lock:       mpi=Yes & gpu=No & debug=No & gcov=No & unified=No & single=No & mixed=No & fastmath=No
+    Git:        18b7dcc7ad3a66260613dd23a226cb2e258257d4 on viscous-stress-and-ellipse-ib (clean)
+
+post_process:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : OFF
+        SIMULATION    : OFF
+        POST_PROCESS  : ON
+        SYSCHECK      : OFF
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+simulation:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : OFF
+        SIMULATION    : ON
+        POST_PROCESS  : OFF
+        SYSCHECK      : OFF
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+pre_process:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : ON
+        SIMULATION    : OFF
+        POST_PROCESS  : OFF
+        SYSCHECK      : OFF
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+syscheck:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : OFF
+        SIMULATION    : OFF
+        POST_PROCESS  : OFF
+        SYSCHECK      : ON
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+CPU:
+
+    CPU Info:
+    From lscpu
+    Architecture:                            x86_64
+    CPU op-mode(s):                          32-bit, 64-bit
+    Address sizes:                           46 bits physical, 48 bits virtual
+    Byte Order:                              Little Endian
+    CPU(s):                                  20
+    On-line CPU(s) list:                     0-19
+    Vendor ID:                               GenuineIntel
+    Model name:                              12th Gen Intel(R) Core(TM) i7-12700K
+    CPU family:                              6
+    Model:                                   151
+    Thread(s) per core:                      2
+    Core(s) per socket:                      12
+    Socket(s):                               1
+    Stepping:                                2
+    CPU(s) scaling MHz:                      23%
+    CPU max MHz:                             5100.0000
+    CPU min MHz:                             800.0000
+    BogoMIPS:                                7219.20
+    Flags:                                   fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault cat_l2 cdp_l2 ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid rdt_a rdseed adx smap clflushopt clwb intel_pt sha_ni xsaveopt xsavec xgetbv1 xsaves split_lock_detect user_shstk avx_vnni dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp hwp_pkg_req hfi vnmi umip pku ospke waitpkg gfni vaes vpclmulqdq rdpid movdiri movdir64b fsrm md_clear serialize pconfig arch_lbr ibt flush_l1d arch_capabilities
+    Virtualization:                          VT-x
+    L1d cache:                               512 KiB (12 instances)
+    L1i cache:                               512 KiB (12 instances)
+    L2 cache:                                12 MiB (9 instances)
+    L3 cache:                                25 MiB (1 instance)
+    NUMA node(s):                            1
+    NUMA node0 CPU(s):                       0-19
+    Vulnerability Gather data sampling:      Not affected
+    Vulnerability Ghostwrite:                Not affected
+    Vulnerability Indirect target selection: Not affected
+    Vulnerability Itlb multihit:             Not affected
+    Vulnerability L1tf:                      Not affected
+    Vulnerability Mds:                       Not affected
+    Vulnerability Meltdown:                  Not affected
+    Vulnerability Mmio stale data:           Not affected
+    Vulnerability Reg file data sampling:    Mitigation; Clear Register File
+    Vulnerability Retbleed:                  Not affected
+    Vulnerability Spec rstack overflow:      Not affected
+    Vulnerability Spec store bypass:         Mitigation; Speculative Store Bypass disabled via prctl
+    Vulnerability Spectre v1:                Mitigation; usercopy/swapgs barriers and __user pointer sanitization
+    Vulnerability Spectre v2:                Mitigation; Enhanced / Automatic IBRS; IBPB conditional; PBRSB-eIBRS SW sequence; BHI BHI_DIS_S
+    Vulnerability Srbds:                     Not affected
+    Vulnerability Tsa:                       Not affected
+    Vulnerability Tsx async abort:           Not affected
+    Vulnerability Vmscape:                   Mitigation; IBPB before exit to userspace
+
diff --git a/tests/5600D63B/golden.txt b/tests/5600D63B/golden.txt
new file mode 100644
index 0000000000..8cafaa4276
--- /dev/null
+++ b/tests/5600D63B/golden.txt
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diff --git a/tests/7FA04E95/golden-metadata.txt b/tests/7FA04E95/golden-metadata.txt
new file mode 100644
index 0000000000..31c6dd7a52
--- /dev/null
+++ b/tests/7FA04E95/golden-metadata.txt
@@ -0,0 +1,193 @@
+This file was created on 2026-01-09 16:27:49.075261.
+
+mfc.sh:
+
+    Invocation: test --generate -o 7FA04E95
+    Lock:       mpi=Yes & gpu=No & debug=No & gcov=No & unified=No & single=No & mixed=No & fastmath=No
+    Git:        18b7dcc7ad3a66260613dd23a226cb2e258257d4 on viscous-stress-and-ellipse-ib (clean)
+
+syscheck:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : OFF
+        SIMULATION    : OFF
+        POST_PROCESS  : OFF
+        SYSCHECK      : ON
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+simulation:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : OFF
+        SIMULATION    : ON
+        POST_PROCESS  : OFF
+        SYSCHECK      : OFF
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+pre_process:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : ON
+        SIMULATION    : OFF
+        POST_PROCESS  : OFF
+        SYSCHECK      : OFF
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+post_process:
+
+    CMake Configuration:
+    
+        CMake v3.28.3 on schwarzschild
+    
+        C       : GNU v13.3.0 (/usr/bin/cc)
+        Fortran : GNU v13.3.0 (/usr/bin/gfortran)
+    
+        PRE_PROCESS   : OFF
+        SIMULATION    : OFF
+        POST_PROCESS  : ON
+        SYSCHECK      : OFF
+        DOCUMENTATION : OFF
+        ALL           : OFF
+    
+        MPI     : ON
+        OpenACC : OFF
+        OpenMP  : OFF
+    
+        Fypp    : /home/dan/Documents/repos/MFC/build/venv/bin/fypp
+        Doxygen : 
+    
+        Build Type : Release
+    
+    Configuration Environment:
+    
+        CC       : /usr/bin/cc
+        CXX      : /usr/bin/c++
+        FC       : /usr/bin/gfortran
+        OMPI_CC  : 
+        OMPI_CXX : 
+        OMPI_FC  : 
+
+CPU:
+
+    CPU Info:
+    From lscpu
+    Architecture:                            x86_64
+    CPU op-mode(s):                          32-bit, 64-bit
+    Address sizes:                           46 bits physical, 48 bits virtual
+    Byte Order:                              Little Endian
+    CPU(s):                                  20
+    On-line CPU(s) list:                     0-19
+    Vendor ID:                               GenuineIntel
+    Model name:                              12th Gen Intel(R) Core(TM) i7-12700K
+    CPU family:                              6
+    Model:                                   151
+    Thread(s) per core:                      2
+    Core(s) per socket:                      12
+    Socket(s):                               1
+    Stepping:                                2
+    CPU(s) scaling MHz:                      18%
+    CPU max MHz:                             5100.0000
+    CPU min MHz:                             800.0000
+    BogoMIPS:                                7219.20
+    Flags:                                   fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault cat_l2 cdp_l2 ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid rdt_a rdseed adx smap clflushopt clwb intel_pt sha_ni xsaveopt xsavec xgetbv1 xsaves split_lock_detect user_shstk avx_vnni dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp hwp_pkg_req hfi vnmi umip pku ospke waitpkg gfni vaes vpclmulqdq rdpid movdiri movdir64b fsrm md_clear serialize pconfig arch_lbr ibt flush_l1d arch_capabilities
+    Virtualization:                          VT-x
+    L1d cache:                               512 KiB (12 instances)
+    L1i cache:                               512 KiB (12 instances)
+    L2 cache:                                12 MiB (9 instances)
+    L3 cache:                                25 MiB (1 instance)
+    NUMA node(s):                            1
+    NUMA node0 CPU(s):                       0-19
+    Vulnerability Gather data sampling:      Not affected
+    Vulnerability Ghostwrite:                Not affected
+    Vulnerability Indirect target selection: Not affected
+    Vulnerability Itlb multihit:             Not affected
+    Vulnerability L1tf:                      Not affected
+    Vulnerability Mds:                       Not affected
+    Vulnerability Meltdown:                  Not affected
+    Vulnerability Mmio stale data:           Not affected
+    Vulnerability Reg file data sampling:    Mitigation; Clear Register File
+    Vulnerability Retbleed:                  Not affected
+    Vulnerability Spec rstack overflow:      Not affected
+    Vulnerability Spec store bypass:         Mitigation; Speculative Store Bypass disabled via prctl
+    Vulnerability Spectre v1:                Mitigation; usercopy/swapgs barriers and __user pointer sanitization
+    Vulnerability Spectre v2:                Mitigation; Enhanced / Automatic IBRS; IBPB conditional; PBRSB-eIBRS SW sequence; BHI BHI_DIS_S
+    Vulnerability Srbds:                     Not affected
+    Vulnerability Tsa:                       Not affected
+    Vulnerability Tsx async abort:           Not affected
+    Vulnerability Vmscape:                   Mitigation; IBPB before exit to userspace
+
diff --git a/tests/7FA04E95/golden.txt b/tests/7FA04E95/golden.txt
new file mode 100644
index 0000000000..28b8f8e315
--- /dev/null
+++ b/tests/7FA04E95/golden.txt
@@ -0,0 +1,11 @@
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\ No newline at end of file

From f7c2577ab4cc0c8388bec7e5f6231213c80b0b5a Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 16:29:55 -0500
Subject: [PATCH 24/34] spelling and formatting

---
 src/common/m_compute_levelset.fpp  |  12 +--
 src/common/m_ib_patches.fpp        |   5 +-
 src/simulation/m_ibm.fpp           |  82 ++++++++++----------
 src/simulation/m_rhs.fpp           |  20 ++---
 src/simulation/m_time_steppers.fpp |   2 +-
 src/simulation/m_viscous.fpp       | 120 ++++++++++++++---------------
 6 files changed, 120 insertions(+), 121 deletions(-)

diff --git a/src/common/m_compute_levelset.fpp b/src/common/m_compute_levelset.fpp
index 69ddda5fd5..c7a3df21cf 100644
--- a/src/common/m_compute_levelset.fpp
+++ b/src/common/m_compute_levelset.fpp
@@ -361,8 +361,8 @@ contains
         inverse_rotation(:, :) = patch_ib(ib_patch_id)%rotation_matrix_inverse(:, :)
         rotation(:, :) = patch_ib(ib_patch_id)%rotation_matrix(:, :)
 
-        ellipse_coeffs(1) = 0.5_wp * length_x
-        ellipse_coeffs(2) = 0.5_wp * length_y
+        ellipse_coeffs(1) = 0.5_wp*length_x
+        ellipse_coeffs(2) = 0.5_wp*length_y
 
         $:GPU_PARALLEL_LOOP(private='[i,j,k,idx,quadratic_coeffs,xy_local,normal_vector]', &
                   & copyin='[ib_patch_id,center,ellipse_coeffs,inverse_rotation,rotation]', collapse=2)
@@ -375,17 +375,17 @@ contains
                 if ((xy_local(1)/ellipse_coeffs(1))**2 + (xy_local(2)/ellipse_coeffs(2))**2 <= 1._wp) then
 
                     normal_vector = xy_local
-                    normal_vector(2) = normal_vector(2) * (ellipse_coeffs(1)/ellipse_coeffs(2))**2._wp ! get the normal direction via the coordinate transofmration method
-                    normal_vector = normal_vector / sqrt(dot_product(normal_vector, normal_vector)) ! normalize the vector
+                    normal_vector(2) = normal_vector(2)*(ellipse_coeffs(1)/ellipse_coeffs(2))**2._wp ! get the normal direction via the coordinate transformation method
+                    normal_vector = normal_vector/sqrt(dot_product(normal_vector, normal_vector)) ! normalize the vector
                     levelset_norm%sf(i, j, 0, ib_patch_id, :) = matmul(rotation, normal_vector) ! save after rotating the vector to the global frame
 
                     ! use the normal vector to set up the quadratic equation for the levelset, using A, B, and C in indices 1, 2, and 3
                     quadratic_coeffs(1) = (normal_vector(1)/ellipse_coeffs(1))**2 + (normal_vector(2)/ellipse_coeffs(2))**2
-                    quadratic_coeffs(2) = 2._wp * ((xy_local(1)*normal_vector(1)/(ellipse_coeffs(1)**2)) + (xy_local(2)*normal_vector(2)/(ellipse_coeffs(2)**2)))
+                    quadratic_coeffs(2) = 2._wp*((xy_local(1)*normal_vector(1)/(ellipse_coeffs(1)**2)) + (xy_local(2)*normal_vector(2)/(ellipse_coeffs(2)**2)))
                     quadratic_coeffs(3) = (xy_local(1)/ellipse_coeffs(1))**2._wp + (xy_local(2)/ellipse_coeffs(2))**2._wp - 1._wp
 
                     ! compute the levelset with the quadratic equation [ -B + sqrt(B^2 - 4AC) ] / 2A
-                    levelset%sf(i, j, 0, ib_patch_id) = -0.5_wp * (-quadratic_coeffs(2) + sqrt(quadratic_coeffs(2)**2._wp - 4._wp * quadratic_coeffs(1)*quadratic_coeffs(3))) / quadratic_coeffs(1)
+                    levelset%sf(i, j, 0, ib_patch_id) = -0.5_wp*(-quadratic_coeffs(2) + sqrt(quadratic_coeffs(2)**2._wp - 4._wp*quadratic_coeffs(1)*quadratic_coeffs(3)))/quadratic_coeffs(1)
                 end if
             end do
         end do
diff --git a/src/common/m_ib_patches.fpp b/src/common/m_ib_patches.fpp
index 8468d0b859..9d22479ab2 100644
--- a/src/common/m_ib_patches.fpp
+++ b/src/common/m_ib_patches.fpp
@@ -765,7 +765,6 @@ contains
 
     end subroutine s_ib_cylinder
 
-
     subroutine s_ib_ellipse(patch_id, ib_markers_sf)
 
         integer, intent(in) :: patch_id
@@ -780,8 +779,8 @@ contains
         ! Transferring the rectangle's centroid and length information
         center(1) = patch_ib(patch_id)%x_centroid
         center(2) = patch_ib(patch_id)%y_centroid
-        ellipse_coeffs(1) = 0.5_wp * patch_ib(patch_id)%length_x
-        ellipse_coeffs(2) = 0.5_wp * patch_ib(patch_id)%length_y
+        ellipse_coeffs(1) = 0.5_wp*patch_ib(patch_id)%length_x
+        ellipse_coeffs(2) = 0.5_wp*patch_ib(patch_id)%length_y
         inverse_rotation(:, :) = patch_ib(patch_id)%rotation_matrix_inverse(:, :)
 
         ! Checking whether the rectangle covers a particular cell in the
diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 6105a43b3f..2ddc3580f7 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -98,7 +98,7 @@ contains
         moving_immersed_boundary_flag = .false.
         do i = 1, num_ibs
             if (patch_ib(i)%moving_ibm /= 0) then
-              call s_compute_moment_of_inertia(i, patch_ib(i)%angular_vel)
+                call s_compute_moment_of_inertia(i, patch_ib(i)%angular_vel)
                 moving_immersed_boundary_flag = .true.
             end if
             call s_update_ib_rotation_matrix(i)
@@ -207,16 +207,16 @@ contains
                     if (patch_id /= 0) then
                         q_prim_vf(E_idx)%sf(j, k, l) = 1._wp
                         if (patch_ib(patch_id)%moving_ibm > 0._wp) then
-                              rho = 0._wp
-                              do i = 1, num_fluids
-                                  rho = rho + q_prim_vf(contxb+i-1)%sf(j, k, l)
-                              end do
-
-                              ! Sets thhe momentum
-                              do i = 1, num_dims
-                                  q_cons_vf(momxb+i-1)%sf(j, k, l) = patch_ib(patch_id)%vel(i) * rho
-                                  q_prim_vf(momxb+i-1)%sf(j, k, l) = patch_ib(patch_id)%vel(i)
-                              end do
+                            rho = 0._wp
+                            do i = 1, num_fluids
+                                rho = rho + q_prim_vf(contxb + i - 1)%sf(j, k, l)
+                            end do
+
+                            ! Sets the momentum
+                            do i = 1, num_dims
+                                q_cons_vf(momxb + i - 1)%sf(j, k, l) = patch_ib(patch_id)%vel(i)*rho
+                                q_prim_vf(momxb + i - 1)%sf(j, k, l) = patch_ib(patch_id)%vel(i)
+                            end do
                         end if
                     end if
                 end do
@@ -1022,7 +1022,7 @@ contains
 
         integer :: gp_id, i, j, k, l, q, ib_idx
         real(wp), dimension(num_ibs, 3) :: forces, torques
-        real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2 ! viscous stress tensor with temp vectors to hold divergence calculations 
+        real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2 ! viscous stress tensor with temp vectors to hold divergence calculations
         real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution, vel
         real(wp) :: cell_volume, dx, dy, dz
 
@@ -1045,16 +1045,16 @@ contains
                         dy = y_cc(j + 1) - y_cc(j)
 
                         ! Get the pressure contribution to force via a finite difference to compute the 2D components of the gradient of the pressure and cell volume
-                        local_force_contribution(1) = -1._wp * (q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx) ! force is the negative pressure gradient
-                        local_force_contribution(2) = -1._wp * (q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
+                        local_force_contribution(1) = -1._wp*(q_prim_vf(E_idx)%sf(i + 1, j, k) - q_prim_vf(E_idx)%sf(i - 1, j, k))/(2._wp*dx) ! force is the negative pressure gradient
+                        local_force_contribution(2) = -1._wp*(q_prim_vf(E_idx)%sf(i, j + 1, k) - q_prim_vf(E_idx)%sf(i, j - 1, k))/(2._wp*dy)
                         cell_volume = abs(dx*dy)
                         ! add the 3D component of the pressure gradient, if we are working in 3 dimensions
                         if (num_dims == 3) then
                             dz = z_cc(k + 1) - z_cc(k)
-                            local_force_contribution(3) = -1._wp * (q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
+                            local_force_contribution(3) = -1._wp*(q_prim_vf(E_idx)%sf(i, j, k + 1) - q_prim_vf(E_idx)%sf(i, j, k - 1))/(2._wp*dz)
                             cell_volume = abs(cell_volume*dz)
                         else
-                          local_force_contribution(3) = 0._wp
+                            local_force_contribution(3) = 0._wp
                         end if
 
                         ! Update the force values atomically to prevent race conditions
@@ -1065,41 +1065,41 @@ contains
                         ! if (.false.) then
                         if (viscous) then
                             ! get the linear force component first
-                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i-1, j, k)
-                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i+1, j, k)
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the viscous stress tensor
-                            local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x componenets of the derivative to the force
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i - 1, j, k)
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i + 1, j, k)
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dx) ! get the x derivative of the viscous stress tensor
+                            local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x components of the derivative to the force
                             do l = 1, 3
-                                ! take the cross products for the torque componenet
+                                ! take the cross products for the torque component
                                 call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
                                 call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
                             end do
 
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dx) ! get the x derivative of the cross product
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dx) ! get the x derivative of the cross product
                             local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
-                            
-                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j-1, k)
-                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j+1, k)
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy)
+
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j - 1, k)
+                            call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j + 1, k)
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dy)
                             local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
                             do l = 1, 3
                                 call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
                                 call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
                             end do
 
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dy) 
+                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dy)
                             local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(2, 1:3)
 
                             if (num_dims == 3) then
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j, k-1)
-                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j, k+1)
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j, k - 1)
+                                call s_compute_viscous_stress_tensor(viscous_stress_div_2, q_prim_vf, dynamic_viscosity, i, j, k + 1)
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dz)
                                 local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
                                 do l = 1, 3
                                     call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
                                     call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
                                 end do
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1) / (2._wp * dz) 
+                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dz)
                                 local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(3, 1:3)
                             end if
                         end if
@@ -1122,15 +1122,15 @@ contains
 
         ! consider body forces after reducing to avoid double counting
         do i = 1, num_ibs
-          if (bf_x) then
-              forces(i, 1) = forces(i, 1) + accel_bf(1)*patch_ib(i)%mass
-          end if
-          if (bf_y) then
-              forces(i, 2) = forces(i, 2) + accel_bf(2)*patch_ib(i)%mass
-          end if
-          if (bf_z) then
-              forces(i, 3) = forces(i, 3) + accel_bf(3)*patch_ib(i)%mass
-          end if
+            if (bf_x) then
+                forces(i, 1) = forces(i, 1) + accel_bf(1)*patch_ib(i)%mass
+            end if
+            if (bf_y) then
+                forces(i, 2) = forces(i, 2) + accel_bf(2)*patch_ib(i)%mass
+            end if
+            if (bf_z) then
+                forces(i, 3) = forces(i, 3) + accel_bf(3)*patch_ib(i)%mass
+            end if
         end do
 
         ! apply the summed forces
@@ -1171,7 +1171,7 @@ contains
 
         ! if the IB is in 2D or a 3D sphere, we can compute this exactly
         if (patch_ib(ib_marker)%geometry == 2) then ! circle
-            patch_ib(ib_marker)%moment = 0.5_wp * patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2
+            patch_ib(ib_marker)%moment = 0.5_wp*patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%radius)**2
         elseif (patch_ib(ib_marker)%geometry == 3) then ! rectangle
             patch_ib(ib_marker)%moment = patch_ib(ib_marker)%mass*(patch_ib(ib_marker)%length_x**2 + patch_ib(ib_marker)%length_y**2)/6._wp
         elseif (patch_ib(ib_marker)%geometry == 6) then ! ellipse
diff --git a/src/simulation/m_rhs.fpp b/src/simulation/m_rhs.fpp
index 78570fc2ff..eb6f70cf11 100644
--- a/src/simulation/m_rhs.fpp
+++ b/src/simulation/m_rhs.fpp
@@ -1636,18 +1636,18 @@ contains
                 if (viscous) then
                     if (p > 0) then
                         call s_compute_viscous_stress_cylindrical_boundary(q_prim_vf, &
-                                                             dq_prim_dx_vf(mom_idx%beg:mom_idx%end), &
-                                                             dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
-                                                             dq_prim_dz_vf(mom_idx%beg:mom_idx%end), &
-                                                             tau_Re_vf, &
-                                                             idwbuff(1), idwbuff(2), idwbuff(3))
+                                                                           dq_prim_dx_vf(mom_idx%beg:mom_idx%end), &
+                                                                           dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
+                                                                           dq_prim_dz_vf(mom_idx%beg:mom_idx%end), &
+                                                                           tau_Re_vf, &
+                                                                           idwbuff(1), idwbuff(2), idwbuff(3))
                     else
                         call s_compute_viscous_stress_cylindrical_boundary(q_prim_vf, &
-                                                             dq_prim_dx_vf(mom_idx%beg:mom_idx%end), &
-                                                             dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
-                                                             dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
-                                                             tau_Re_vf, &
-                                                             idwbuff(1), idwbuff(2), idwbuff(3))
+                                                                           dq_prim_dx_vf(mom_idx%beg:mom_idx%end), &
+                                                                           dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
+                                                                           dq_prim_dy_vf(mom_idx%beg:mom_idx%end), &
+                                                                           tau_Re_vf, &
+                                                                           idwbuff(1), idwbuff(2), idwbuff(3))
                     end if
 
                     $:GPU_PARALLEL_LOOP(private='[i,j,l]', collapse=2)
diff --git a/src/simulation/m_time_steppers.fpp b/src/simulation/m_time_steppers.fpp
index 1a6b1fd18c..b196b3afa3 100644
--- a/src/simulation/m_time_steppers.fpp
+++ b/src/simulation/m_time_steppers.fpp
@@ -627,7 +627,7 @@ contains
 
                             if (patch_ib(i)%moving_ibm == 2) then ! if we are using two-way coupling, apply force and torque
                                 ! compute the force and torque on the IB from the fluid
-                                call s_compute_ib_forces(q_prim_vf, 1._wp / fluid_pp(1)%Re(1))
+                                call s_compute_ib_forces(q_prim_vf, 1._wp/fluid_pp(1)%Re(1))
 
                                 ! update the velocity from the force value
                                 patch_ib(i)%vel = patch_ib(i)%vel + rk_coef(s, 3)*dt*(patch_ib(i)%force/patch_ib(i)%mass)/rk_coef(s, 4)
diff --git a/src/simulation/m_viscous.fpp b/src/simulation/m_viscous.fpp
index 855befec84..c6b053bdaf 100644
--- a/src/simulation/m_viscous.fpp
+++ b/src/simulation/m_viscous.fpp
@@ -21,7 +21,7 @@ module m_viscous
     use m_finite_differences
 
     private; public s_get_viscous, &
-    s_compute_viscous_stress_cylindrical_boundary, &
+ s_compute_viscous_stress_cylindrical_boundary, &
  s_initialize_viscous_module, &
  s_reconstruct_cell_boundary_values_visc_deriv, &
  s_finalize_viscous_module, &
@@ -62,8 +62,8 @@ contains
     !  @param grad_y_vf Cell-average primitive variable derivatives, y-dir
     !  @param grad_z_vf Cell-average primitive variable derivatives, z-dir
     subroutine s_compute_viscous_stress_cylindrical_boundary(q_prim_vf, grad_x_vf, grad_y_vf, grad_z_vf, &
-                                               tau_Re_vf, &
-                                               ix, iy, iz)
+                                                             tau_Re_vf, &
+                                                             ix, iy, iz)
 
         type(scalar_field), dimension(sys_size), intent(in) :: q_prim_vf
         type(scalar_field), dimension(num_dims), intent(in) :: grad_x_vf, grad_y_vf, grad_z_vf
@@ -1514,63 +1514,63 @@ contains
 
     ! computes the viscous stress tensor at a particule i, j, k element
     subroutine s_compute_viscous_stress_tensor(viscous_stress_tensor, q_prim_vf, dynamic_viscosity, i, j, k)
-      $:GPU_ROUTINE(parallelism='[seq]')
-
-      real(wp), dimension(1:3, 1:3), intent(inout) :: viscous_stress_tensor
-      type(scalar_field), dimension(1:sys_size), intent(in) :: q_prim_vf
-      real(wp), intent(in) :: dynamic_viscosity
-      integer, intent(in) :: i, j, k
-
-      real(wp), dimension(1:3, 1:3) :: velocity_gradient_tensor
-      real(wp), dimension(1:3) :: dx
-      real(wp) :: divergence
-      integer :: l, q ! iterators
-
-      ! zero the viscous stress, collection of velocity diriviatives, and spacial finite differences
-      viscous_stress_tensor = 0._wp
-      velocity_gradient_tensor = 0._wp
-      dx = 0._wp
-
-      ! get the change in x used in the finite difference equaiont
-      dx(1) = 0.5_wp * (x_cc(i+1) - x_cc(i-1))
-      dx(2) = 0.5_wp * (y_cc(j+1) - y_cc(j-1))
-      if (num_dims == 3) then
-          dx(3) = 0.5_wp * (z_cc(k+1) - z_cc(k-1))
-      end if
-
-      ! compute the velocity gradient tensor
-      do l = 1, num_dims
-          velocity_gradient_tensor(l,1) = (q_prim_vf(momxb+l-1)%sf(i+1, j, k) - q_prim_vf(momxb+l-1)%sf(i-1, j, k)) / (2._wp * dx(1)) 
-          velocity_gradient_tensor(l,2) = (q_prim_vf(momxb+l-1)%sf(i, j+1, k) - q_prim_vf(momxb+l-1)%sf(i, j-1, k)) / (2._wp * dx(2))
-          if (num_dims == 3) then
-              velocity_gradient_tensor(l,3) = (q_prim_vf(momxb+l-1)%sf(i, j, k+1) - q_prim_vf(momxb+l-1)%sf(i, j, k-1)) / (2._wp * dx(3)) 
-          end if
-      end do
-
-      ! compute divergence
-      divergence = 0._wp
-      do l = 1, num_dims
-          divergence = divergence + velocity_gradient_tensor(l, l)
-      end do
-
-      ! set up the shear stress tensor
-      do l = 1, num_dims
-          do q = 1, num_dims
-              viscous_stress_tensor(l, q) = dynamic_viscosity * (velocity_gradient_tensor(l,q) + velocity_gradient_tensor(q,l))
-          end do
-      end do
-
-      ! populate the viscous_stress_tensor
-      do l = 1, num_dims
-          viscous_stress_tensor(l, l) = viscous_stress_tensor(l, l) - 2._wp * divergence * dynamic_viscosity / 3._wp
-      end do
-
-      if (num_dims == 2) then
-          do l = 1, 3
-              viscous_stress_tensor(3, l) = 0._wp
-              viscous_stress_tensor(l, 3) = 0._wp
-          end do
-      end if
+        $:GPU_ROUTINE(parallelism='[seq]')
+
+        real(wp), dimension(1:3, 1:3), intent(inout) :: viscous_stress_tensor
+        type(scalar_field), dimension(1:sys_size), intent(in) :: q_prim_vf
+        real(wp), intent(in) :: dynamic_viscosity
+        integer, intent(in) :: i, j, k
+
+        real(wp), dimension(1:3, 1:3) :: velocity_gradient_tensor
+        real(wp), dimension(1:3) :: dx
+        real(wp) :: divergence
+        integer :: l, q ! iterators
+
+        ! zero the viscous stress, collection of velocity diriviatives, and spacial finite differences
+        viscous_stress_tensor = 0._wp
+        velocity_gradient_tensor = 0._wp
+        dx = 0._wp
+
+        ! get the change in x used in the finite difference equaiont
+        dx(1) = 0.5_wp*(x_cc(i + 1) - x_cc(i - 1))
+        dx(2) = 0.5_wp*(y_cc(j + 1) - y_cc(j - 1))
+        if (num_dims == 3) then
+            dx(3) = 0.5_wp*(z_cc(k + 1) - z_cc(k - 1))
+        end if
+
+        ! compute the velocity gradient tensor
+        do l = 1, num_dims
+            velocity_gradient_tensor(l, 1) = (q_prim_vf(momxb + l - 1)%sf(i + 1, j, k) - q_prim_vf(momxb + l - 1)%sf(i - 1, j, k))/(2._wp*dx(1))
+            velocity_gradient_tensor(l, 2) = (q_prim_vf(momxb + l - 1)%sf(i, j + 1, k) - q_prim_vf(momxb + l - 1)%sf(i, j - 1, k))/(2._wp*dx(2))
+            if (num_dims == 3) then
+                velocity_gradient_tensor(l, 3) = (q_prim_vf(momxb + l - 1)%sf(i, j, k + 1) - q_prim_vf(momxb + l - 1)%sf(i, j, k - 1))/(2._wp*dx(3))
+            end if
+        end do
+
+        ! compute divergence
+        divergence = 0._wp
+        do l = 1, num_dims
+            divergence = divergence + velocity_gradient_tensor(l, l)
+        end do
+
+        ! set up the shear stress tensor
+        do l = 1, num_dims
+            do q = 1, num_dims
+                viscous_stress_tensor(l, q) = dynamic_viscosity*(velocity_gradient_tensor(l, q) + velocity_gradient_tensor(q, l))
+            end do
+        end do
+
+        ! populate the viscous_stress_tensor
+        do l = 1, num_dims
+            viscous_stress_tensor(l, l) = viscous_stress_tensor(l, l) - 2._wp*divergence*dynamic_viscosity/3._wp
+        end do
+
+        if (num_dims == 2) then
+            do l = 1, 3
+                viscous_stress_tensor(3, l) = 0._wp
+                viscous_stress_tensor(l, 3) = 0._wp
+            end do
+        end if
 
     end subroutine s_compute_viscous_stress_tensor
 

From e909026d788d5484e6ed8d999de4504804f8a222 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 16:32:26 -0500
Subject: [PATCH 25/34] examples need to be commited for formatting as well

---
 examples/2D_mibm_shock_cylinder/case.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/examples/2D_mibm_shock_cylinder/case.py b/examples/2D_mibm_shock_cylinder/case.py
index b962b0c269..0ca5cbb635 100644
--- a/examples/2D_mibm_shock_cylinder/case.py
+++ b/examples/2D_mibm_shock_cylinder/case.py
@@ -2,7 +2,7 @@
 import math
 
 # This case is a recreation of the case from "Moving overlapping grids with adaptive mesh refinement for high-speed reactive and non-reactive flow"
-# by William D. Henshaw and Donald W. Schwendeman 
+# by William D. Henshaw and Donald W. Schwendeman
 
 # fluid parameters
 gam_a = 1.4
@@ -16,7 +16,7 @@
 post_shock_density = 2.6069
 post_shock_speed = 0.6944
 
-domain_size = 4.
+domain_size = 4.0
 wave_front = -1.5
 
 total_time = 1.5
@@ -90,32 +90,32 @@
             "parallel_io": "T",
             # Patch: Constant Tube filled with air
             # Specify the cylindrical air tube grid geometry
-            "patch_icpp(1)%geometry": 3,            
+            "patch_icpp(1)%geometry": 3,
             "patch_icpp(2)%geometry": 3,
-            # patch locations      
+            # patch locations
             "patch_icpp(1)%x_centroid": 0.5 * wave_front + 0.25 * domain_size,
-            "patch_icpp(1)%y_centroid": 0.,
+            "patch_icpp(1)%y_centroid": 0.0,
             "patch_icpp(1)%length_x": 0.5 * domain_size - wave_front,
             "patch_icpp(1)%length_y": domain_size,
             "patch_icpp(2)%x_centroid": 0.5 * wave_front - 0.25 * domain_size,
-            "patch_icpp(2)%y_centroid": 0.,
+            "patch_icpp(2)%y_centroid": 0.0,
             "patch_icpp(2)%length_x": 0.5 * domain_size + wave_front,
             "patch_icpp(2)%length_y": domain_size,
             # Specify the patch primitive variables
             "patch_icpp(1)%vel(1)": pre_shock_speed,
             "patch_icpp(1)%vel(2)": 0.0,
             "patch_icpp(1)%pres": pre_shock_pressure,
-            "patch_icpp(1)%alpha_rho(1)":  pre_shock_density,
+            "patch_icpp(1)%alpha_rho(1)": pre_shock_density,
             "patch_icpp(1)%alpha(1)": 1.0e00,
             "patch_icpp(2)%vel(1)": post_shock_speed,
             "patch_icpp(2)%vel(2)": 0.0,
             "patch_icpp(2)%pres": post_shock_pressure,
-            "patch_icpp(2)%alpha_rho(1)":  post_shock_density,
+            "patch_icpp(2)%alpha_rho(1)": post_shock_density,
             "patch_icpp(2)%alpha(1)": 1.0e00,
             # Patch: Cylinder Immersed Boundary
             "patch_ib(1)%geometry": 2,
             "patch_ib(1)%x_centroid": -0.5,
-            "patch_ib(1)%y_centroid": 0.,
+            "patch_ib(1)%y_centroid": 0.0,
             "patch_ib(1)%radius": 0.5,
             "patch_ib(1)%slip": "T",
             "patch_ib(1)%moving_ibm": 2,

From 5b3b328fd7352a5faa88353ee5e09c80ddf55309 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 16:36:33 -0500
Subject: [PATCH 26/34] fixed normalization error in numeric moment of inertia
 calculation

---
 src/simulation/m_ibm.fpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 2ddc3580f7..176ebfd350 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1203,7 +1203,7 @@ contains
                             end if
 
                             ! project the position along the axis to find the closest distance to the rotation axis
-                            closest_point_along_axis = normal_axis*dot_product(axis, position)
+                            closest_point_along_axis = normal_axis*dot_product(normal_axis, position)
                             vector_to_axis = position - closest_point_along_axis
                             distance_to_axis = dot_product(vector_to_axis, vector_to_axis) ! saves the distance to the axis squared
 

From e5cd3547d0229e36b57f5e18a9d6b8fd04108a97 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 16:38:53 -0500
Subject: [PATCH 27/34] The normal axis in 2D is always z-hat

---
 src/simulation/m_ibm.fpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 176ebfd350..78243fa58c 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1160,7 +1160,7 @@ contains
         integer :: i, j, k, count
 
         if (p == 0) then
-            normal_axis = [0, 1, 0]
+            normal_axis = [0, 0, 1]
         else if (sqrt(sum(axis**2)) == 0) then
             ! if the object is not actually rotating at this time, return a dummy value and exit
             patch_ib(ib_marker)%moment = 1._wp

From 7da350d961bcc5392c00b4521c4a9065d37a1999 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Fri, 9 Jan 2026 16:55:05 -0500
Subject: [PATCH 28/34] Cleared an old TODO for pre-process checking the
 ellipse patch

---
 src/pre_process/m_check_ib_patches.fpp | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/pre_process/m_check_ib_patches.fpp b/src/pre_process/m_check_ib_patches.fpp
index 19493814e5..55595b0e98 100644
--- a/src/pre_process/m_check_ib_patches.fpp
+++ b/src/pre_process/m_check_ib_patches.fpp
@@ -63,7 +63,7 @@ contains
                          patch_ib(i)%geometry == 12) then
                     call s_check_model_ib_patch_geometry(i)
                 else if (patch_ib(i)%geometry == 6) then
-                    print *, "Ellipse Patch"
+                    call s_check_ellipse_ib_patch_geometry(i)
                 else
                     call s_prohibit_abort("Invalid IB patch", &
                                           "patch_ib("//trim(iStr)//")%geometry must be "// &
@@ -94,6 +94,25 @@ contains
             .or. f_is_default(patch_ib(patch_id)%y_centroid), &
             'in circle IB patch '//trim(iStr))
 
+    end subroutine s_check_circle_ib_patch_geometry
+
+        !>  This subroutine verifies that the geometric parameters of
+        !!      the circle patch have consistently been inputted by the
+        !!      user.
+        !!  @param patch_id Patch identifier
+    impure subroutine s_check_ellipse_ib_patch_geometry(patch_id)
+
+        integer, intent(in) :: patch_id
+
+        call s_int_to_str(patch_id, iStr)
+
+        @:PROHIBIT(n == 0 .or. p > 0 &
+            .or. patch_ib(patch_id)%length_x <= 0._wp &
+            .or. patch_ib(patch_id)%length_y <= 0._wp &
+            .or. f_is_default(patch_ib(patch_id)%x_centroid) &
+            .or. f_is_default(patch_ib(patch_id)%y_centroid), &
+            'in ellipse IB patch '//trim(iStr))
+
     end subroutine s_check_circle_ib_patch_geometry
 
     !>  This subroutine verifies that the geometric parameters of

From 3c41c90e90b7201851d234fabc46675ec372e67b Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Sat, 10 Jan 2026 09:09:30 -0500
Subject: [PATCH 29/34] Error in ellipse ib patch check

---
 src/pre_process/m_check_ib_patches.fpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pre_process/m_check_ib_patches.fpp b/src/pre_process/m_check_ib_patches.fpp
index 55595b0e98..25077feaf1 100644
--- a/src/pre_process/m_check_ib_patches.fpp
+++ b/src/pre_process/m_check_ib_patches.fpp
@@ -113,7 +113,7 @@ contains
             .or. f_is_default(patch_ib(patch_id)%y_centroid), &
             'in ellipse IB patch '//trim(iStr))
 
-    end subroutine s_check_circle_ib_patch_geometry
+    end subroutine s_check_ellipse_ib_patch_geometry
 
     !>  This subroutine verifies that the geometric parameters of
         !!      the airfoil patch have consistently been inputted by the

From 137376d502a1c00c529c852f65695345ca5b79bf Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Sat, 10 Jan 2026 09:14:39 -0500
Subject: [PATCH 30/34] Ran formatting again

---
 src/pre_process/m_check_ib_patches.fpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/pre_process/m_check_ib_patches.fpp b/src/pre_process/m_check_ib_patches.fpp
index 25077feaf1..1b09929dda 100644
--- a/src/pre_process/m_check_ib_patches.fpp
+++ b/src/pre_process/m_check_ib_patches.fpp
@@ -96,8 +96,8 @@ contains
 
     end subroutine s_check_circle_ib_patch_geometry
 
-        !>  This subroutine verifies that the geometric parameters of
-        !!      the circle patch have consistently been inputted by the
+    !>  This subroutine verifies that the geometric parameters of
+        !!      the ellipse patch have consistently been inputted by the
         !!      user.
         !!  @param patch_id Patch identifier
     impure subroutine s_check_ellipse_ib_patch_geometry(patch_id)

From e262ef9387a432cc58ead795fa521c27e17e29be Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Sat, 10 Jan 2026 09:27:51 -0500
Subject: [PATCH 31/34] Took recomendation for undefined behavior of same
 vector for in/out

---
 src/simulation/m_ibm.fpp | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 78243fa58c..8242227f13 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1023,13 +1023,13 @@ contains
         integer :: gp_id, i, j, k, l, q, ib_idx
         real(wp), dimension(num_ibs, 3) :: forces, torques
         real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2 ! viscous stress tensor with temp vectors to hold divergence calculations
-        real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution, vel
+        real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution, vel, viscous_cross_1, viscous_cross_2
         real(wp) :: cell_volume, dx, dy, dz
 
         forces = 0._wp
         torques = 0._wp
 
-        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity]', collapse=3)
+        $:GPU_PARALLEL_LOOP(private='[ib_idx,radial_vector,local_force_contribution,cell_volume,local_torque_contribution, viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, viscous_cross_1, viscous_cross_2, dx, dy, dz]', copy='[forces,torques]', copyin='[ib_markers,patch_ib,dynamic_viscosity]', collapse=3)
         do i = 0, m
             do j = 0, n
                 do k = 0, p
@@ -1071,11 +1071,11 @@ contains
                             local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(1, 1:3) ! add te x components of the derivative to the force
                             do l = 1, 3
                                 ! take the cross products for the torque component
-                                call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                                call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                                call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_cross_1(l, 1:3))
+                                call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_cross_2(l, 1:3))
                             end do
 
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dx) ! get the x derivative of the cross product
+                            viscous_stress_div = (viscous_cross_2 - viscous_cross_1)/(2._wp*dx) ! get the x derivative of the cross product
                             local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(1, 1:3) ! apply the cross product derivative to the torque
 
                             call s_compute_viscous_stress_tensor(viscous_stress_div_1, q_prim_vf, dynamic_viscosity, i, j - 1, k)
@@ -1083,11 +1083,11 @@ contains
                             viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dy)
                             local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(2, 1:3)
                             do l = 1, 3
-                                call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                                call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                                call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_cross_1(l, 1:3))
+                                call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_cross_2(l, 1:3))
                             end do
 
-                            viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dy)
+                            viscous_stress_div = (viscous_cross_2 - viscous_cross_1)/(2._wp*dy)
                             local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(2, 1:3)
 
                             if (num_dims == 3) then
@@ -1096,10 +1096,10 @@ contains
                                 viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dz)
                                 local_force_contribution(1:3) = local_force_contribution(1:3) + viscous_stress_div(3, 1:3)
                                 do l = 1, 3
-                                    call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_stress_div_1(l, 1:3))
-                                    call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_stress_div_2(l, 1:3))
+                                    call s_cross_product(radial_vector, viscous_stress_div_1(l, 1:3), viscous_cross_1(l, 1:3))
+                                    call s_cross_product(radial_vector, viscous_stress_div_2(l, 1:3), viscous_cross_2(l, 1:3))
                                 end do
-                                viscous_stress_div = (viscous_stress_div_2 - viscous_stress_div_1)/(2._wp*dz)
+                                viscous_stress_div = (viscous_cross_2 - viscous_cross_1)/(2._wp*dz)
                                 local_torque_contribution(1:3) = local_torque_contribution(1:3) + viscous_stress_div(3, 1:3)
                             end if
                         end if

From 8e6ba64e0d3557eec57d7026bf007216cf2cd978 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Sat, 10 Jan 2026 09:31:06 -0500
Subject: [PATCH 32/34] Fixed build error

---
 src/simulation/m_ibm.fpp           |  4 ++--
 tests/5600D63B/golden-metadata.txt | 30 +++++++++++++++---------------
 tests/7FA04E95/golden-metadata.txt | 30 +++++++++++++++---------------
 3 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 8242227f13..4cad91de5e 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -1022,8 +1022,8 @@ contains
 
         integer :: gp_id, i, j, k, l, q, ib_idx
         real(wp), dimension(num_ibs, 3) :: forces, torques
-        real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2 ! viscous stress tensor with temp vectors to hold divergence calculations
-        real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution, vel, viscous_cross_1, viscous_cross_2
+        real(wp), dimension(1:3, 1:3) :: viscous_stress_div, viscous_stress_div_1, viscous_stress_div_2, viscous_cross_1, viscous_cross_2 ! viscous stress tensor with temp vectors to hold divergence calculations
+        real(wp), dimension(1:3) :: local_force_contribution, radial_vector, local_torque_contribution, vel
         real(wp) :: cell_volume, dx, dy, dz
 
         forces = 0._wp
diff --git a/tests/5600D63B/golden-metadata.txt b/tests/5600D63B/golden-metadata.txt
index 87feb7fece..54dc299d7b 100644
--- a/tests/5600D63B/golden-metadata.txt
+++ b/tests/5600D63B/golden-metadata.txt
@@ -1,12 +1,12 @@
-This file was created on 2026-01-09 16:23:05.537791.
+This file was created on 2026-01-10 09:29:50.350999.
 
 mfc.sh:
 
     Invocation: test --generate -o 5600D63B
     Lock:       mpi=Yes & gpu=No & debug=No & gcov=No & unified=No & single=No & mixed=No & fastmath=No
-    Git:        18b7dcc7ad3a66260613dd23a226cb2e258257d4 on viscous-stress-and-ellipse-ib (clean)
+    Git:        e262ef9387a432cc58ead795fa521c27e17e29be on viscous-stress-and-ellipse-ib (dirty)
 
-post_process:
+pre_process:
 
     CMake Configuration:
     
@@ -15,9 +15,9 @@ post_process:
         C       : GNU v13.3.0 (/usr/bin/cc)
         Fortran : GNU v13.3.0 (/usr/bin/gfortran)
     
-        PRE_PROCESS   : OFF
+        PRE_PROCESS   : ON
         SIMULATION    : OFF
-        POST_PROCESS  : ON
+        POST_PROCESS  : OFF
         SYSCHECK      : OFF
         DOCUMENTATION : OFF
         ALL           : OFF
@@ -40,7 +40,7 @@ post_process:
         OMPI_CXX : 
         OMPI_FC  : 
 
-simulation:
+syscheck:
 
     CMake Configuration:
     
@@ -50,9 +50,9 @@ simulation:
         Fortran : GNU v13.3.0 (/usr/bin/gfortran)
     
         PRE_PROCESS   : OFF
-        SIMULATION    : ON
+        SIMULATION    : OFF
         POST_PROCESS  : OFF
-        SYSCHECK      : OFF
+        SYSCHECK      : ON
         DOCUMENTATION : OFF
         ALL           : OFF
     
@@ -74,7 +74,7 @@ simulation:
         OMPI_CXX : 
         OMPI_FC  : 
 
-pre_process:
+simulation:
 
     CMake Configuration:
     
@@ -83,8 +83,8 @@ pre_process:
         C       : GNU v13.3.0 (/usr/bin/cc)
         Fortran : GNU v13.3.0 (/usr/bin/gfortran)
     
-        PRE_PROCESS   : ON
-        SIMULATION    : OFF
+        PRE_PROCESS   : OFF
+        SIMULATION    : ON
         POST_PROCESS  : OFF
         SYSCHECK      : OFF
         DOCUMENTATION : OFF
@@ -108,7 +108,7 @@ pre_process:
         OMPI_CXX : 
         OMPI_FC  : 
 
-syscheck:
+post_process:
 
     CMake Configuration:
     
@@ -119,8 +119,8 @@ syscheck:
     
         PRE_PROCESS   : OFF
         SIMULATION    : OFF
-        POST_PROCESS  : OFF
-        SYSCHECK      : ON
+        POST_PROCESS  : ON
+        SYSCHECK      : OFF
         DOCUMENTATION : OFF
         ALL           : OFF
     
@@ -160,7 +160,7 @@ CPU:
     Core(s) per socket:                      12
     Socket(s):                               1
     Stepping:                                2
-    CPU(s) scaling MHz:                      23%
+    CPU(s) scaling MHz:                      32%
     CPU max MHz:                             5100.0000
     CPU min MHz:                             800.0000
     BogoMIPS:                                7219.20
diff --git a/tests/7FA04E95/golden-metadata.txt b/tests/7FA04E95/golden-metadata.txt
index 31c6dd7a52..5464c03831 100644
--- a/tests/7FA04E95/golden-metadata.txt
+++ b/tests/7FA04E95/golden-metadata.txt
@@ -1,12 +1,12 @@
-This file was created on 2026-01-09 16:27:49.075261.
+This file was created on 2026-01-10 09:30:46.874399.
 
 mfc.sh:
 
     Invocation: test --generate -o 7FA04E95
     Lock:       mpi=Yes & gpu=No & debug=No & gcov=No & unified=No & single=No & mixed=No & fastmath=No
-    Git:        18b7dcc7ad3a66260613dd23a226cb2e258257d4 on viscous-stress-and-ellipse-ib (clean)
+    Git:        e262ef9387a432cc58ead795fa521c27e17e29be on viscous-stress-and-ellipse-ib (dirty)
 
-syscheck:
+simulation:
 
     CMake Configuration:
     
@@ -16,9 +16,9 @@ syscheck:
         Fortran : GNU v13.3.0 (/usr/bin/gfortran)
     
         PRE_PROCESS   : OFF
-        SIMULATION    : OFF
+        SIMULATION    : ON
         POST_PROCESS  : OFF
-        SYSCHECK      : ON
+        SYSCHECK      : OFF
         DOCUMENTATION : OFF
         ALL           : OFF
     
@@ -40,7 +40,7 @@ syscheck:
         OMPI_CXX : 
         OMPI_FC  : 
 
-simulation:
+pre_process:
 
     CMake Configuration:
     
@@ -49,8 +49,8 @@ simulation:
         C       : GNU v13.3.0 (/usr/bin/cc)
         Fortran : GNU v13.3.0 (/usr/bin/gfortran)
     
-        PRE_PROCESS   : OFF
-        SIMULATION    : ON
+        PRE_PROCESS   : ON
+        SIMULATION    : OFF
         POST_PROCESS  : OFF
         SYSCHECK      : OFF
         DOCUMENTATION : OFF
@@ -74,7 +74,7 @@ simulation:
         OMPI_CXX : 
         OMPI_FC  : 
 
-pre_process:
+post_process:
 
     CMake Configuration:
     
@@ -83,9 +83,9 @@ pre_process:
         C       : GNU v13.3.0 (/usr/bin/cc)
         Fortran : GNU v13.3.0 (/usr/bin/gfortran)
     
-        PRE_PROCESS   : ON
+        PRE_PROCESS   : OFF
         SIMULATION    : OFF
-        POST_PROCESS  : OFF
+        POST_PROCESS  : ON
         SYSCHECK      : OFF
         DOCUMENTATION : OFF
         ALL           : OFF
@@ -108,7 +108,7 @@ pre_process:
         OMPI_CXX : 
         OMPI_FC  : 
 
-post_process:
+syscheck:
 
     CMake Configuration:
     
@@ -119,8 +119,8 @@ post_process:
     
         PRE_PROCESS   : OFF
         SIMULATION    : OFF
-        POST_PROCESS  : ON
-        SYSCHECK      : OFF
+        POST_PROCESS  : OFF
+        SYSCHECK      : ON
         DOCUMENTATION : OFF
         ALL           : OFF
     
@@ -160,7 +160,7 @@ CPU:
     Core(s) per socket:                      12
     Socket(s):                               1
     Stepping:                                2
-    CPU(s) scaling MHz:                      18%
+    CPU(s) scaling MHz:                      29%
     CPU max MHz:                             5100.0000
     CPU min MHz:                             800.0000
     BogoMIPS:                                7219.20

From 626451875770df5e19e141eaac32311b7a8b6a49 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Sat, 10 Jan 2026 09:34:15 -0500
Subject: [PATCH 33/34] Fixed integer comparison with real

---
 src/simulation/m_ibm.fpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/simulation/m_ibm.fpp b/src/simulation/m_ibm.fpp
index 4cad91de5e..0b8ec1ab81 100644
--- a/src/simulation/m_ibm.fpp
+++ b/src/simulation/m_ibm.fpp
@@ -206,7 +206,7 @@ contains
                     patch_id = ib_markers%sf(j, k, l)
                     if (patch_id /= 0) then
                         q_prim_vf(E_idx)%sf(j, k, l) = 1._wp
-                        if (patch_ib(patch_id)%moving_ibm > 0._wp) then
+                        if (patch_ib(patch_id)%moving_ibm > 0) then
                             rho = 0._wp
                             do i = 1, num_fluids
                                 rho = rho + q_prim_vf(contxb + i - 1)%sf(j, k, l)

From ae1c63c785de3b8b25b5b74b61baab5ac153da11 Mon Sep 17 00:00:00 2001
From: danieljvickers <dnlvickers5@gmail.com>
Date: Sat, 10 Jan 2026 09:37:44 -0500
Subject: [PATCH 34/34] Small changed

---
 src/common/m_ib_patches.fpp | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/src/common/m_ib_patches.fpp b/src/common/m_ib_patches.fpp
index 9d22479ab2..1bb00c44a3 100644
--- a/src/common/m_ib_patches.fpp
+++ b/src/common/m_ib_patches.fpp
@@ -776,17 +776,15 @@ contains
         real(wp), dimension(1:2) :: center !< x and y coordinates in local IB frame
         real(wp), dimension(1:3, 1:3) :: inverse_rotation
 
-        ! Transferring the rectangle's centroid and length information
+        ! Transferring the ellipse's centroid and length information
         center(1) = patch_ib(patch_id)%x_centroid
         center(2) = patch_ib(patch_id)%y_centroid
         ellipse_coeffs(1) = 0.5_wp*patch_ib(patch_id)%length_x
         ellipse_coeffs(2) = 0.5_wp*patch_ib(patch_id)%length_y
         inverse_rotation(:, :) = patch_ib(patch_id)%rotation_matrix_inverse(:, :)
 
-        ! Checking whether the rectangle covers a particular cell in the
-        ! domain and verifying whether the current patch has the permission
-        ! to write to that cell. If both queries check out, the primitive
-        ! variables of the current patch are assigned to this cell.
+        ! Checking whether the ellipse covers a particular cell in the
+        ! domain
         $:GPU_PARALLEL_LOOP(private='[i,j, xy_local]', copy='[ib_markers_sf]',&
                   & copyin='[patch_id,center,ellipse_coeffs,inverse_rotation,x_cc,y_cc]', collapse=2)
         do j = 0, n