Fix comment typos, remove dead code, apply ffmt S102/S081 formatting

Author: sbryngelson

src/common/include/1dHardcodedIC.fpp

@@ -5,7 +5,7 @@
 
 #:def Hardcoded1D()
     select case (patch_icpp(patch_id)%hcid)
-    case (150) ! 1D Smooth Alfven Case for MHD
+    case (150)  ! 1D Smooth Alfven Case for MHD
         ! velocity
         q_prim_vf(momxb + 1)%sf(i, 0, 0) = 0.1_wp*sin(2._wp*pi*x_cc(i))
         q_prim_vf(momxb + 2)%sf(i, 0, 0) = 0.1_wp*cos(2._wp*pi*x_cc(i))

src/common/include/2dHardcodedIC.fpp

@@ -17,19 +17,17 @@
 #:enddef
 
 #:def Hardcoded2D()
-    select case (patch_icpp(patch_id)%hcid) ! 2D_hardcoded_ic example case
+    select case (patch_icpp(patch_id)%hcid)  ! 2D_hardcoded_ic example case
     case (200)
         if (y_cc(j) <= (-x_cc(i)**3 + 1)**(1._wp/3._wp)) then
             ! Volume Fractions
             q_prim_vf(advxb)%sf(i, j, 0) = eps
             q_prim_vf(advxe)%sf(i, j, 0) = 1._wp - eps
-            ! Densities
             q_prim_vf(contxb)%sf(i, j, 0) = eps*1000._wp
             q_prim_vf(contxe)%sf(i, j, 0) = (1._wp - eps)*1._wp
-            ! Pressure
             q_prim_vf(E_idx)%sf(i, j, 0) = 1000._wp
         end if
-    case (202) ! Gresho vortex (Gouasmi et al 2022 JCP)
+    case (202)  ! Gresho vortex (Gouasmi et al 2022 JCP)
         r = ((x_cc(i) - 0.5_wp)**2 + (y_cc(j) - 0.5_wp)**2)**0.5_wp
         rmax = 0.2_wp
 
@@ -50,7 +48,7 @@
             q_prim_vf(momxe)%sf(i, j, 0) = 0._wp
             q_prim_vf(E_idx)%sf(i, j, 0) = p0 + umax**2*(-2 + 4*log(2._wp))
         end if
-    case (203) ! Gresho vortex (Gouasmi et al 2022 JCP) with density correction
+    case (203)  ! Gresho vortex (Gouasmi et al 2022 JCP) with density correction
         r = ((x_cc(i) - 0.5_wp)**2._wp + (y_cc(j) - 0.5_wp)**2)**0.5_wp
         rmax = 0.2_wp
 
@@ -73,7 +71,7 @@
         end if
 
         q_prim_vf(contxb)%sf(i, j, 0) = q_prim_vf(E_idx)%sf(i, j, 0)**(1._wp/gam)
-    case (204) ! Rayleigh-Taylor instability
+    case (204)  ! Rayleigh-Taylor instability
         rhoH = 3._wp
         rhoL = 1._wp
         pRef = 1.e5_wp
@@ -104,10 +102,10 @@
             pInt = pref + rhoH*9.81_wp*(1.2_wp - intH)
             q_prim_vf(E_idx)%sf(i, j, 0) = pInt + rhoL*9.81_wp*(intH - y_cc(j))
         end if
-    case (205) ! 2D lung wave interaction problem
-        h = 0.0_wp ! non dim origin y
-        lam = 1.0_wp ! non dim lambda
-        amp = patch_icpp(patch_id)%a(2) ! to be changed later!       !non dim amplitude
+    case (205)  ! 2D lung wave interaction problem
+        h = 0.0_wp  ! non dim origin y
+        lam = 1.0_wp  ! non dim lambda
+        amp = patch_icpp(patch_id)%a(2)  ! to be changed later!       !non dim amplitude
 
         intH = amp*sin(2*pi*x_cc(i)/lam - pi/2) + h
 
@@ -118,26 +116,26 @@
             q_prim_vf(advxb)%sf(i, j, 0) = patch_icpp(1)%alpha(1)
             q_prim_vf(advxe)%sf(i, j, 0) = patch_icpp(1)%alpha(2)
         end if
-    case (206) ! 2D lung wave interaction problem - horizontal domain
-        h = 0.0_wp ! non dim origin y
-        lam = 1.0_wp ! non dim lambda
+    case (206)  ! 2D lung wave interaction problem - horizontal domain
+        h = 0.0_wp  ! non dim origin y
+        lam = 1.0_wp  ! non dim lambda
         amp = patch_icpp(patch_id)%a(2)
 
         intL = amp*sin(2*pi*y_cc(j)/lam - pi/2) + h
 
-        if (x_cc(i) > intL) then ! this is the liquid
+        if (x_cc(i) > intL) then  ! this is the liquid
             q_prim_vf(contxb)%sf(i, j, 0) = patch_icpp(1)%alpha_rho(1)
             q_prim_vf(contxe)%sf(i, j, 0) = patch_icpp(1)%alpha_rho(2)
             q_prim_vf(E_idx)%sf(i, j, 0) = patch_icpp(1)%pres
             q_prim_vf(advxb)%sf(i, j, 0) = patch_icpp(1)%alpha(1)
             q_prim_vf(advxe)%sf(i, j, 0) = patch_icpp(1)%alpha(2)
         end if
-    case (207) ! Kelvin Helmholtz Instability
+    case (207)  ! Kelvin Helmholtz Instability
         sigma = 0.05_wp/sqrt(2.0_wp)
         gauss1 = exp(-(y_cc(j) - 0.75_wp)**2/(2.0_wp*sigma**2))
         gauss2 = exp(-(y_cc(j) - 0.25_wp)**2/(2.0_wp*sigma**2))
         q_prim_vf(momxb + 1)%sf(i, j, 0) = 0.1_wp*sin(4.0_wp*pi*x_cc(i))*(gauss1 + gauss2)
-    case (208) ! Richtmeyer Meshkov Instability
+    case (208)  ! Richtmeyer Meshkov Instability
         lam = 1.0_wp
         eps = 1.0e-6_wp
         ei = 5.0_wp
@@ -152,7 +150,7 @@
             q_prim_vf(advxb)%sf(i, j, 0) = alpha_sf6
             q_prim_vf(advxe)%sf(i, j, 0) = alpha_air
         end if
-    case (250) ! MHD Orszag-Tang vortex
+    case (250)  ! MHD Orszag-Tang vortex
         ! gamma = 5/3 rho = 25/(36*pi) p = 5/(12*pi) v = (-sin(2*pi*y), sin(2*pi*x), 0) B = (-sin(2*pi*y)/sqrt(4*pi),
         ! sin(4*pi*x)/sqrt(4*pi), 0)
 
@@ -161,7 +159,7 @@
 
         q_prim_vf(B_idx%beg)%sf(i, j, 0) = -sin(2._wp*pi*y_cc(j))/sqrt(4._wp*pi)
         q_prim_vf(B_idx%beg + 1)%sf(i, j, 0) = sin(4._wp*pi*x_cc(i))/sqrt(4._wp*pi)
-    case (251) ! RMHD Cylindrical Blast Wave [Mignone, 2006: Section 4.3.1]
+    case (251)  ! RMHD Cylindrical Blast Wave [Mignone, 2006: Section 4.3.1]
         if (x_cc(i)**2 + y_cc(j)**2 < 0.08_wp**2) then
             q_prim_vf(contxb)%sf(i, j, 0) = 0.01
             q_prim_vf(E_idx)%sf(i, j, 0) = 1.0
@@ -176,7 +174,7 @@
         end if
 
         ! case 252 is for the 2D MHD Rotor problem
-    case (252) ! 2D MHD Rotor Problem
+    case (252)  ! 2D MHD Rotor Problem
         ! Ambient conditions are set in the JSON file. This case imposes the dense, rotating cylinder.
         !
         ! gamma = 1.4 Ambient medium (r > 0.1): rho = 1, p = 1, v = 0, B = (1,0,0) Rotor (r <= 0.1): rho = 10, p = 1 v has angular
@@ -202,7 +200,7 @@
             q_prim_vf(momxb)%sf(i, j, 0) = -(2._wp/sqrt(r_sq))*(y_cc(j) - 0.5_wp)*(0.115_wp - sqrt(r_sq))/(0.015_wp)
             q_prim_vf(momxb + 1)%sf(i, j, 0) = (2._wp/sqrt(r_sq))*(x_cc(i) - 0.5_wp)*(0.115_wp - sqrt(r_sq))/(0.015_wp)
         end if
-    case (253) ! MHD Smooth Magnetic Vortex
+    case (253)  ! MHD Smooth Magnetic Vortex
         ! Section 5.2 of Implicit hybridized discontinuous Galerkin methods for compressible magnetohydrodynamics C. Ciuca, P.
         ! Fernandez, A. Christophe, N.C. Nguyen, J. Peraire
 
@@ -217,7 +215,7 @@
         ! pressure
         q_prim_vf(E_idx)%sf(i, j, &
                   & 0) = 1._wp + (1 - 2._wp*(x_cc(i)**2 + y_cc(j)**2))*exp(1 - (x_cc(i)**2 + y_cc(j)**2))/((2._wp*pi)**3)
-    case (260) ! Gaussian Divergence Pulse
+    case (260)  ! Gaussian Divergence Pulse
         ! Bx(x) = 1 + C * erf((x-0.5)/\sigma) => \partialBx/\partialx = C * (2/\sqrt\pi) * exp[-((x-0.5)/\sigma)**2] * (1/\sigma)
         ! Choose C = \epsilon * \sigma * \sqrt\pi / 2 => \partialBx/\partialx = \epsilon * exp[-((x-0.5)/\sigma)**2] \psi is
         ! initialized to zero everywhere.
@@ -228,7 +226,7 @@
 
         ! B-field
         q_prim_vf(B_idx%beg)%sf(i, j, 0) = 1._wp + C_mhd*erf((x_cc(i) - 0.5_wp)/sigma)
-    case (261) ! Blob
+    case (261)  ! Blob
         r0 = 1._wp/sqrt(8._wp)
         r2 = x_cc(i)**2 + y_cc(j)**2
         r = sqrt(r2)
@@ -239,7 +237,7 @@
             ! q_prim_vf(B_idx%beg)%sf(i,j,0) = 1._wp/(4._wp*pi) * (alpha**8 - 2._wp*alpha**4 + 1._wp) q_prim_vf(E_idx)%sf(i,j,0) =
             ! 6._wp - q_prim_vf(B_idx%beg)%sf(i,j,0)**2/2._wp
         end if
-    case (262) ! Tilted 2D MHD shock‐tube at α = arctan2 (≈63.4°)
+    case (262)  ! Tilted 2D MHD shock‐tube at α = arctan2 (≈63.4°)
         ! rotate by \alpha = atan(2)
         alpha = atan(2._wp)
         cosA = cos(alpha)

src/common/include/3dHardcodedIC.fpp

@@ -7,13 +7,13 @@
     real(wp), dimension(:), allocatable :: y_th_arr, z_th_arr, r_th_arr
     ! Variables to describe initial condition of jet
     real(wp)                      :: r, ux_th, ux_am, p_th, p_am, rho_th, rho_am, y_th, z_th, r_th, eps_smooth
-    real(wp)                      :: rcut, xcut ! Intermediate variables for creating smooth initial condition
+    real(wp)                      :: rcut, xcut  ! Intermediate variables for creating smooth initial condition
     real(wp), dimension(0:n, 0:p) :: rcut_arr
-    integer                       :: l, q, s ! Iterators for reading input files
-    integer                       :: start, end ! Ints to keep track of position in file
-    character(len=1000)           :: line ! String to store line in file
-    character(len=25)             :: value ! String to store value in line
-    integer                       :: NJet ! Number of jets
+    integer                       :: l, q, s  ! Iterators for reading input files
+    integer                       :: start, end  ! Ints to keep track of position in file
+    character(len=1000)           :: line  ! String to store line in file
+    character(len=25)             :: value  ! String to store value in line
+    integer                       :: NJet  ! Number of jets
 
     eps = 1e-9_wp
 
@@ -29,19 +29,19 @@
 
         open (unit=10, file="jets.csv", status="old", action="read")
         do q = 0, NJet - 1
-            read (10, '(A)') line ! Read a full line as a string
+            read (10, '(A)') line  ! Read a full line as a string
             start = 1
 
             do l = 0, 2
-                end = index(line(start:), ',') ! Find the next comma
+                end = index(line(start:), ',')  ! Find the next comma
                 if (end == 0) then
-                    value = trim(adjustl(line(start:))) ! Last value in the line
+                    value = trim(adjustl(line(start:)))  ! Last value in the line
                 else
-                    value = trim(adjustl(line(start:start + end - 2))) ! Extract substring
-                    start = start + end ! Move to next value
+                    value = trim(adjustl(line(start:start + end - 2)))  ! Extract substring
+                    start = start + end  ! Move to next value
                 end if
                 if (l == 0) then
-                    read (value, *) y_th_arr(q) ! Convert string to numeric value
+                    read (value, *) y_th_arr(q)  ! Convert string to numeric value
                 else if (l == 1) then
                     read (value, *) z_th_arr(q)
                 else
@@ -66,7 +66,7 @@
 
 #:def Hardcoded3D()
     select case (patch_icpp(patch_id)%hcid)
-    case (300) ! Rayleigh-Taylor instability
+    case (300)  ! Rayleigh-Taylor instability
         rhoH = 3._wp
         rhoL = 1._wp
         pRef = 1.e5_wp
@@ -97,7 +97,7 @@
             pInt = pref + rhoH*9.81_wp*(1.2_wp - intH)
             q_prim_vf(E_idx)%sf(i, j, k) = pInt + rhoL*9.81_wp*(intH - y_cc(j))
         end if
-    case (301) ! (3D lung geometry in X direction, |sin(*)+sin(*)|)
+    case (301)  ! (3D lung geometry in X direction, |sin(*)+sin(*)|)
         h = 0.0_wp
         lam = 1.0_wp
         amp = patch_icpp(patch_id)%a(2)
@@ -109,7 +109,7 @@
             q_prim_vf(advxb)%sf(i, j, k) = patch_icpp(1)%alpha(1)
             q_prim_vf(advxe)%sf(i, j, k) = patch_icpp(1)%alpha(2)
         end if
-    case (302) ! 3D Jet with IGR
+    case (302)  ! 3D Jet with IGR
         ux_th = 10*sqrt(1.4*0.4)
         ux_am = 0.0*sqrt(1.4)
         p_th = 2.0_wp
@@ -139,7 +139,7 @@
         end if
 
         q_prim_vf(E_idx)%sf(i, j, k) = p_th*rcut*xcut + p_am
-    case (303) ! 3D Multijet
+    case (303)  ! 3D Multijet
         eps_smooth = 3.0_wp
         ux_th = 10*sqrt(1.4*0.4)
         ux_am = 2.5*sqrt(1.4*0.4)

src/common/include/ExtrusionHardcodedIC.fpp

@@ -40,18 +40,18 @@
     integer                                 :: f, iter, ios, ios2, unit, unit2, idx, idy, index_x, index_y, jump, line_count, ycount
     real(wp)                                :: x_len, x_step, y_len, y_step
     real(wp)                                :: dummy_x, dummy_y, dummy_z, x0, y0
-    integer                                 :: global_offset_x, global_offset_y ! MPI subdomain offset
+    integer                                 :: global_offset_x, global_offset_y  ! MPI subdomain offset
     real(wp)                                :: delta_x, delta_y
-    character(len=100), dimension(sys_size) :: fileNames ! Arrays to store all data from files
+    character(len=100), dimension(sys_size) :: fileNames  ! Arrays to store all data from files
     character(len=200)                      :: errmsg
     real(wp), allocatable                   :: stored_values(:,:,:)
     real(wp), allocatable                   :: x_coords(:), y_coords(:)
     logical                                 :: files_loaded = .false.
     real(wp)                                :: domain_xstart, domain_xend, domain_ystart, domain_yend
-    character(len=*), parameter             :: init_dir = "/home/MFC/FilesDirectory" ! For example /home/MFC/examples/1D_Shock/D/
-    character(len=20)                       :: file_num_str ! For storing the file number as a string
-    character(len=20)                       :: zeros_part ! For the trailing zeros part
-    character(len=6), parameter             :: zeros_default = "000000" ! Default zeros (can be changed)
+    character(len=*), parameter             :: init_dir = "/home/MFC/FilesDirectory"  ! For example /home/MFC/examples/1D_Shock/D/
+    character(len=20)                       :: file_num_str  ! For storing the file number as a string
+    character(len=20)                       :: zeros_part  ! For the trailing zeros part
+    character(len=6), parameter             :: zeros_default = "000000"  ! Default zeros (can be changed)
 #:enddef
 
 #:def HardcodedReadValues()
@@ -67,7 +67,7 @@
         if (ios2 /= 0) call s_mpi_abort("Error opening file: " // trim(fileNames(1)))
 
         select case (num_dims)
-        case (1, 2) ! 1D and 2D cases are similar
+        case (1, 2)  ! 1D and 2D cases are similar
             ! Count lines
             line_count = 0
             do
@@ -100,7 +100,7 @@
             x_step = x_cc(1) - x_cc(0)
             delta_x = merge(x_cc(0) - domain_xstart + x_step/2.0, x_cc(index_x) - domain_xstart + x_step/2.0, num_dims == 1)
             global_offset_x = nint(abs(delta_x)/x_step)
-        case (3) ! 3D case - determine grid structure
+        case (3)  ! 3D case - determine grid structure
             ! Find yRows by counting rows with same x
             read (unit2, *, iostat=ios2) x0, y0, dummy_z
             if (ios2 /= 0) call s_mpi_abort("Error reading first line")