cleanup

sbryngelson · sbryngelson · commit c59fc0f293f9 · 2025-01-11T09:28:02.000-05:00
diff --git a/.github/workflows/lint-source.yml b/.github/workflows/lint-source.yml
@@ -42,10 +42,15 @@ jobs:
       run: |
         ! grep -iR -e '\.\.\.' -e '\-\-\-' -e '===' ./src/*
 
+    - name: Looking for all caps comments in source
+      run: |
+        ! grep -RE '^\s+[!]\s+[A-Z]{5}' ./src/*
+
     - name: Looking for junk comments in examples
       run: |
         ! grep -R '# ===' ./benchmarks **/*.py
         ! grep -R '# ===' ./examples/**/*.py
         ! grep -R '==='   ./benchmarks/**/*.py
         ! grep -R '==='   ./examples/**/*.py
 
+
diff --git a/src/post_process/m_data_output.fpp b/src/post_process/m_data_output.fpp
@@ -43,7 +43,6 @@ module m_data_output
 
     ! Including the Silo Fortran interface library that features the subroutines
     ! and parameters that are required to write in the Silo-HDF5 database format
-    ! INCLUDE 'silo.inc'
     include 'silo_f9x.inc'
 
     ! Generic storage for flow variable(s) that are to be written to formatted
diff --git a/src/post_process/m_derived_variables.fpp b/src/post_process/m_derived_variables.fpp
@@ -288,10 +288,6 @@ contains
 
                     if (top == bottom) then
                         slope = 1._wp
-                        !       ELSEIF((top == 0._wp .AND. bottom /= 0._wp) &
-                        !               .OR.            &
-                        !           (bottom == 0._wp .AND. top /= 0._wp)) THEN
-                        !           slope = 0._wp
                     else
                         slope = (top*bottom)/(bottom**2._wp + 1e-16_wp)
                     end if
diff --git a/src/post_process/m_global_parameters.fpp b/src/post_process/m_global_parameters.fpp
@@ -843,13 +843,7 @@ contains
         call MPI_INFO_CREATE(mpi_info_int, ierr)
         call MPI_INFO_SET(mpi_info_int, 'romio_ds_write', 'disable', ierr)
 
-        ! Option for UNIX file system (Hooke/Thomson)
-        ! WRITE(mpiiofs, '(A)') '/ufs_'
-        ! mpiiofs = TRIM(mpiiofs)
-        ! mpi_info_int = MPI_INFO_NULL
-
         allocate (start_idx(1:num_dims))
-
 #endif
 
     end subroutine s_initialize_parallel_io
diff --git a/src/pre_process/m_global_parameters.fpp b/src/pre_process/m_global_parameters.fpp
@@ -834,11 +834,6 @@ contains
         call MPI_INFO_CREATE(mpi_info_int, ierr)
         call MPI_INFO_SET(mpi_info_int, 'romio_ds_write', 'disable', ierr)
 
-        ! Option for UNIX file system (Hooke/Thomson)
-        ! WRITE(mpiiofs, '(A)') '/ufs_'
-        ! mpiiofs = TRIM(mpiiofs)
-        ! mpi_info_int = MPI_INFO_NULL
-
         allocate (start_idx(1:num_dims))
 
 #endif
diff --git a/src/simulation/m_cbc.fpp b/src/simulation/m_cbc.fpp
@@ -98,9 +98,9 @@ module m_cbc
     integer :: cbc_dir, cbc_loc
     !$acc declare create(dj, bcxb, bcxe, bcyb, bcye, bczb, bcze, cbc_dir, cbc_loc)
 
-    !! GRCBC inputs for subsonic inflow and outflow conditions consisting of
-    !! inflow velocities, pressure, density and void fraction as well as
-    !! outflow velocities and pressure
+    ! grCBC inputs for subsonic inflow and outflow conditions consisting of
+    ! inflow velocities, pressure, density and void fraction as well as
+    ! outflow velocities and pressure
 
     real(wp), allocatable, dimension(:) :: pres_in, pres_out, Del_in, Del_out
     real(wp), allocatable, dimension(:, :) :: vel_in, vel_out
@@ -396,13 +396,13 @@ contains
             !$acc update device(bczb, bcze)
         end if
 
-        ! Allocate GRCBC inputs
+        ! Allocate grCBC inputs
         @:ALLOCATE(pres_in(1:num_dims), pres_out(1:num_dims))
         @:ALLOCATE(Del_in(1:num_dims), Del_out(1:num_dims))
         @:ALLOCATE(vel_in(1:num_dims, 1:num_dims), vel_out(1:num_dims, 1:num_dims))
         @:ALLOCATE(alpha_rho_in(1:num_fluids, 1:num_dims), alpha_in(1:num_fluids, 1:num_dims))
 
-        ! Assign and update GRCBC inputs
+        ! Assign and update grCBC inputs
         #:for CBC_DIR, XYZ in [(1, 'x'), (2, 'y'), (3, 'z')]
             if (${CBC_DIR}$ <= num_dims) then
                 vel_in(${CBC_DIR}$, 1) = bc_${XYZ}$%vel_in(1)
@@ -860,7 +860,7 @@ contains
                             call s_compute_nonreflecting_subsonic_buffer_L(lambda, L, rho, c, mf, dalpha_rho_ds, dpres_ds, dvel_ds, dadv_ds)
                         else if ((cbc_loc == -1 .and. bc${XYZ}$b == -7) .or. (cbc_loc == 1 .and. bc${XYZ}$e == -7)) then
                             call s_compute_nonreflecting_subsonic_inflow_L(lambda, L, rho, c, mf, dalpha_rho_ds, dpres_ds, dvel_ds, dadv_ds)
-                            ! Add GRCBC for Subsonic Inflow
+                            ! Add grCBC for Subsonic Inflow
                             if (bc_${XYZ}$%grcbc_in) then
                                 !$acc loop seq
                                 do i = 2, momxb
@@ -880,11 +880,11 @@ contains
                             end if
                         else if ((cbc_loc == -1 .and. bc${XYZ}$b == -8) .or. (cbc_loc == 1 .and. bc${XYZ}$e == -8)) then
                             call s_compute_nonreflecting_subsonic_outflow_L(lambda, L, rho, c, mf, dalpha_rho_ds, dpres_ds, dvel_ds, dadv_ds)
-                            ! Add GRCBC for Subsonic Outflow (Pressure)
+                            ! Add grCBC for Subsonic Outflow (Pressure)
                             if (bc_${XYZ}$%grcbc_out) then
                                 L(advxe) = c*(1._wp - Ma)*(pres - pres_out(${CBC_DIR}$))/Del_out(${CBC_DIR}$)
 
-                                ! Add GRCBC for Subsonic Outflow (Normal Velocity)
+                                ! Add grCBC for Subsonic Outflow (Normal Velocity)
                                 if (bc_${XYZ}$%grcbc_vel_out) then
                                     L(advxe) = L(advxe) + rho*c**2._wp*(1._wp - Ma)*(vel(dir_idx(1)) + vel_out(${CBC_DIR}$, dir_idx(1))*sign(1, cbc_loc))/Del_out(${CBC_DIR}$)
                                 end if
@@ -1536,7 +1536,7 @@ contains
         ! Deallocating the cell-width distribution in the s-direction
         @:DEALLOCATE(ds)
 
-        ! Deallocating GRCBC inputs
+        ! Deallocating grCBC inputs
         @:DEALLOCATE(vel_in, vel_out, pres_in, pres_out, Del_in, Del_out, alpha_rho_in, alpha_in)
 
         ! Deallocating CBC Coefficients in x-direction
diff --git a/src/simulation/m_checker.fpp b/src/simulation/m_checker.fpp
@@ -120,7 +120,7 @@ contains
         @:PROHIBIT(model_eqns == 3 .and. wave_speeds /= 1, "6-equation model (model_eqns = 3) requires wave_speeds = 1")
     end subroutine s_check_inputs_model_eqns
 
-    !> Checks constraints for GRCBC
+    !> Checks constraints for grCBC
     subroutine s_check_inputs_grcbc
         #:for DIR in ['x', 'y', 'z']
             @:PROHIBIT(bc_${DIR}$%grcbc_in .and. (bc_${DIR}$%beg /= -7 .and. bc_${DIR}$%end /= -7), "Subsonic Inflow requires bc = -7")
diff --git a/src/simulation/m_global_parameters.fpp b/src/simulation/m_global_parameters.fpp
@@ -690,7 +690,7 @@ contains
             integral(i)%ymax = dflt_real
         end do
 
-        ! GRCBC flags
+        ! grCBC flags
         #:for dir in {'x', 'y', 'z'}
             bc_${dir}$%grcbc_in = .false.
             bc_${dir}$%grcbc_out = .false.
@@ -1216,11 +1216,6 @@ contains
         call MPI_INFO_CREATE(mpi_info_int, ierr)
         call MPI_INFO_SET(mpi_info_int, 'romio_ds_write', 'disable', ierr)
 
-        ! Option for UNIX file system (Hooke/Thomson)
-        ! WRITE(mpiiofs, '(A)') '/ufs_'
-        ! mpiiofs = TRIM(mpiiofs)
-        ! mpi_info_int = MPI_INFO_NULL
-
         allocate (start_idx(1:num_dims))
 
 #endif
diff --git a/src/simulation/m_hyperelastic.fpp b/src/simulation/m_hyperelastic.fpp
@@ -128,7 +128,8 @@ contains
                         do i = 1, tensor_size
                             tensora(i) = 0_wp
                         end do
-                        ! STEP 1: computing the grad_xi tensor using finite differences
+
+                        ! Step 1: computing the grad_xi tensor using finite differences
                         ! grad_xi definition / organization
                         ! number for the tensor 1-3:  dxix_dx, dxiy_dx, dxiz_dx
                         ! 4-6 :                       dxix_dy, dxiy_dy, dxiz_dy
@@ -148,7 +149,7 @@ contains
                             tensora(8) = tensora(8) + q_prim_vf(xibeg + 1)%sf(j, k, l + r)*fd_coeff_z(r, l)
                             tensora(9) = tensora(9) + q_prim_vf(xiend)%sf(j, k, l + r)*fd_coeff_z(r, l)
                         end do
-                        ! STEP 2a: computing the adjoint of the grad_xi tensor for the inverse
+                        ! Step 2a: computing the adjoint of the grad_xi tensor for the inverse
                         tensorb(1) = tensora(5)*tensora(9) - tensora(6)*tensora(8)
                         tensorb(2) = -(tensora(2)*tensora(9) - tensora(3)*tensora(8))
                         tensorb(3) = tensora(2)*tensora(6) - tensora(3)*tensora(5)
@@ -159,45 +160,45 @@ contains
                         tensorb(8) = -(tensora(1)*tensora(8) - tensora(2)*tensora(7))
                         tensorb(9) = tensora(1)*tensora(5) - tensora(2)*tensora(4)
 
-                        ! STEP 2b: computing the determinant of the grad_xi tensor
+                        ! Step 2b: computing the determinant of the grad_xi tensor
                         tensorb(tensor_size) = tensora(1)*(tensora(5)*tensora(9) - tensora(6)*tensora(8)) &
                                                - tensora(2)*(tensora(4)*tensora(9) - tensora(6)*tensora(7)) &
                                                + tensora(3)*(tensora(4)*tensora(8) - tensora(5)*tensora(7))
 
                         if (tensorb(tensor_size) > verysmall) then
-                            ! STEP 2c: computing the inverse of grad_xi tensor = F
+                            ! Step 2c: computing the inverse of grad_xi tensor = F
                             ! tensorb is the adjoint, tensora becomes F
                             !$acc loop seq
                             do i = 1, tensor_size - 1
                                 tensora(i) = tensorb(i)/tensorb(tensor_size)
                             end do
 
-                            ! STEP 2d: computing the J = det(F) = 1/det(\grad{\xi})
+                            ! Step 2d: computing the J = det(F) = 1/det(\grad{\xi})
                             tensorb(tensor_size) = 1_wp/tensorb(tensor_size)
 
-                            ! STEP 3: computing F transpose F
+                            ! Step 3: computing F transpose F
                             tensorb(1) = tensora(1)**2 + tensora(2)**2 + tensora(3)**2
                             tensorb(5) = tensora(4)**2 + tensora(5)**2 + tensora(6)**2
                             tensorb(9) = tensora(7)**2 + tensora(8)**2 + tensora(9)**2
                             tensorb(2) = tensora(1)*tensora(4) + tensora(2)*tensora(5) + tensora(3)*tensora(6)
                             tensorb(3) = tensora(1)*tensora(7) + tensora(2)*tensora(8) + tensora(3)*tensora(9)
                             tensorb(6) = tensora(4)*tensora(7) + tensora(5)*tensora(8) + tensora(6)*tensora(9)
-                            ! STEP 4: update the btensor, this is consistent with Riemann solvers
+                            ! Step 4: update the btensor, this is consistent with Riemann solvers
                             #:for BIJ, TXY in [(1,1),(2,2),(3,5),(4,3),(5,6),(6,9)]
                                 btensor%vf(${BIJ}$)%sf(j, k, l) = tensorb(${TXY}$)
                             #:endfor
                             ! store the determinant at the last entry of the btensor
                             btensor%vf(b_size)%sf(j, k, l) = tensorb(tensor_size)
-                            ! STEP 5a: updating the Cauchy stress primitive scalar field
+                            ! Step 5a: updating the Cauchy stress primitive scalar field
                             if (hyper_model == 1) then
                                 call s_neoHookean_cauchy_solver(btensor%vf, q_prim_vf, G, j, k, l)
                             elseif (hyper_model == 2) then
                                 call s_Mooney_Rivlin_cauchy_solver(btensor%vf, q_prim_vf, G, j, k, l)
                             end if
-                            ! STEP 5b: updating the pressure field
+                            ! Step 5b: updating the pressure field
                             q_prim_vf(E_idx)%sf(j, k, l) = q_prim_vf(E_idx)%sf(j, k, l) - &
                                                            G*q_prim_vf(xiend + 1)%sf(j, k, l)/gamma
-                            ! STEP 5c: updating the Cauchy stress conservative scalar field
+                            ! Step 5c: updating the Cauchy stress conservative scalar field
                             !$acc loop seq
                             do i = 1, b_size - 1
                                 q_cons_vf(strxb + i - 1)%sf(j, k, l) = &
diff --git a/src/simulation/m_riemann_solvers.fpp b/src/simulation/m_riemann_solvers.fpp
diff --git a/src/simulation/m_sim_helpers.f90 b/src/simulation/m_sim_helpers.f90
diff --git a/src/simulation/m_time_steppers.fpp b/src/simulation/m_time_steppers.fpp
