Renaming icell_ref to icell1

src/SPH2mcfost.f90

@@ -244,7 +244,7 @@ subroutine SPH_to_Voronoi(n_SPH, ndusttypes, particle_id, x,y,z,h, vx,vy,vz, T_g
 
     limit_threshold = (1.0 - SPH_keep_particles) * 0.5 ;
 
-    icell_ref = 1
+    icell1 = 1
 
     write(*,*) "# Farthest particules :"
     write(*,*) "x =", minval(x), maxval(x)

src/benchmarks.f90

@@ -263,7 +263,7 @@ subroutine init_GG_Tau_mol()
      Tcin(icell) = 30.0 * (r_grid(icell)/100.)**(-0.5)
   enddo
 
-  icell = icell_ref
+  icell = icell1
   write(*,*) "Density @ 100 AU", real(densite_gaz(icell) / 100.**3 * (sqrt(r_grid(icell)**2 + z_grid(icell)) / 100.)**2.75)
 
   return
@@ -311,8 +311,8 @@ subroutine init_benchmark_vanZadelhoff1()
 
   !tab_abundance = abundance
 
-  write(*,*) "Density", real(densite_gaz(icell_ref) * &
-       (r_grid(icell_ref)**2 + z_grid(icell_ref)**2)/rmin**2)
+  write(*,*) "Density", real(densite_gaz(icell1) * &
+       (r_grid(icell1)**2 + z_grid(icell1)**2)/rmin**2)
 
   return
 

src/cylindrical_grid.f90

@@ -47,8 +47,6 @@ subroutine build_cylindrical_cell_mapping() ! work also in spherical
     integer :: i,j,k,icell, ntot, ntot2, alloc_status
     integer :: istart,iend,jstart,jend,kstart,kend, istart2,iend2,jstart2,jend2,kstart2,kend2
 
-    icell_ref = 1
-
     istart = 1
     iend = n_rad
 

src/diffusion.f90

@@ -31,7 +31,7 @@ subroutine setDiffusion_coeff(i)
 
   cst_Dcoeff = pi/(12.*sigma)
 
-  p_icell = icell_ref
+  p_icell = icell1
 
   do k=1,n_az
      do j=j_start, nz
@@ -90,7 +90,7 @@ subroutine setDiffusion_coeff0(i)
 
   cst_Dcoeff = pi/(12.*sigma)
 
-  p_icell = icell_ref
+  p_icell = icell1
 
   do k=1,n_az
      do j=j_start,nz
@@ -662,7 +662,7 @@ subroutine compute_Planck_opacities(icell, Planck_opacity,rec_Planck_opacity)
      if (lvariable_dust) then
         p_icell => icell0
      else
-        p_icell => icell_ref
+        p_icell => icell1
      endif
 
      somme  = 0.0_dp
@@ -686,8 +686,8 @@ subroutine compute_Planck_opacities(icell, Planck_opacity,rec_Planck_opacity)
         somme2  = somme2  + B * kappa(p_icell,lambda)
         norm = norm + B*delta_wl
      enddo
-     rec_Planck_opacity = norm/somme * kappa_factor(icell0)
-     Planck_opacity = somme2/norm * kappa_factor(icell0)
+     rec_Planck_opacity = norm/somme * kappa_factor(icell)
+     Planck_opacity = somme2/norm * kappa_factor(icell)
   else
      rec_Planck_opacity = 1e-30
      Planck_opacity = 1e-30

src/disk_physics.f90

@@ -31,7 +31,7 @@ subroutine compute_othin_sublimation_radius()
   cst=cst_th/dust_pop(1)%T_sub
   cst=cst_th/1500.
 
-  icell = icell_ref
+  icell = icell1
 
   do lambda=1, n_lambda
      ! longueur d'onde en metre

src/dust_prop.f90

@@ -811,10 +811,9 @@ subroutine opacite(lambda, p_lambda, no_scatt)
   ! c'est pour les prop de diffusion en relatif donc la veleur exacte n'a pas d'importante
   ldens0 = .false.
   if (.not.lvariable_dust) then
-     icell = icell_ref
-     if (maxval(densite_pouss(:,icell)) < tiny_real) then
+     if (icell_not_empty > icell1) then ! icell1==1
         ldens0 = .true.
-        densite_pouss(:,icell) = densite_pouss(:,icell_not_empty)
+        densite_pouss(:,icell1) = densite_pouss(:,icell_not_empty)
      endif
   endif
 
@@ -1010,8 +1009,7 @@ subroutine opacite(lambda, p_lambda, no_scatt)
 
   ! On remet la densite à zéro si besoin
   if (ldens0) then
-     icell = icell_ref
-     densite_pouss(:,icell) = 0.0_sp
+     densite_pouss(:,icell1) = 0.0_sp
   endif
 
   if ((ldust_prop).and.(lambda == n_lambda)) then
@@ -1055,10 +1053,9 @@ subroutine calc_local_scattering_matrices(lambda, p_lambda)
   ! c'est pour les prop de diffusion en relatif donc la veleur exacte n'a pas d'importante
   ldens0 = .false.
   if (.not.lvariable_dust) then
-     icell = icell_ref
-     if (maxval(densite_pouss(:,icell)) < tiny_real) then
+     if (icell_not_empty > icell1) then
         ldens0 = .true.
-        densite_pouss(:,icell) = densite_pouss(:,icell_not_empty)
+        densite_pouss(:,icell1) = densite_pouss(:,icell_not_empty)
      endif
   endif
 
@@ -1216,8 +1213,7 @@ subroutine calc_local_scattering_matrices(lambda, p_lambda)
   ! see opacite()
   ! On remet la densite à zéro si besoin
   if (ldens0) then
-     icell = icell_ref
-     densite_pouss(:,icell) = 0.0_sp
+     densite_pouss(:,icell1) = 0.0_sp
   endif
 
   return
@@ -1335,8 +1331,14 @@ subroutine write_dust_prop()
   allocate(S11_lambda_theta(n_lambda,0:nang_scatt),pol_lambda_theta(n_lambda,0:nang_scatt))
   allocate(kappa_grain(n_lambda,n_grains_tot))
 
-  icell = icell_not_empty
-  p_icell = icell_ref
+  if (lvariable_dust) then
+     write(*,*) "Warning: dust is not uniform, picking cell #",  icell_not_empty
+     icell = icell_not_empty
+     p_icell = icell_not_empty
+  else
+     icell  = icell_not_empty
+     p_icell = 1
+  endif
 
   kappa_lambda=real((kappa(icell,:)*kappa_factor(icell)/AU_to_cm)/(masse(icell)/(volume(icell)*AU_to_cm**3))) ! cm^2/g
   albedo_lambda=tab_albedo_pos(icell,:)

src/dust_ray_tracing.f90

@@ -503,7 +503,7 @@ subroutine calc_xI_scatt(id,lambda,p_lambda,icell, phik,psup,l,stokes,flag_star)
   if (lvariable_dust) then
      p_icell = icell
   else
-     p_icell = icell_ref
+     p_icell = icell1
   endif
 
   do ibin = 1, RT_n_incl
@@ -565,7 +565,7 @@ subroutine calc_xI_scatt_pola(id,lambda,p_lambda,icell,phik,psup,l,stokes,flag_s
   if (lvariable_dust) then
      p_icell = icell
   else
-     p_icell = icell_ref
+     p_icell = icell1
   endif
 
   do ibin = 1, RT_n_incl
@@ -670,9 +670,9 @@ subroutine init_dust_source_fct1(lambda,ibin,iaz)
   !$omp default(none) &
   !$omp private(icell,p_icell,facteur,kappa_sca,kappa_ext,itype,I_scatt) &
   !$omp shared(n_cells,energie_photon,volume,n_az_rt,n_theta_rt,kappa,kappa_factor,N_type_flux,lambda,iRT) &
-  !$omp shared(J_th,xI_scatt,eps_dust1,lsepar_pola,lsepar_contrib,n_Stokes,nb_proc,tab_albedo_pos,lvariable_dust,icell_ref)
+  !$omp shared(J_th,xI_scatt,eps_dust1,lsepar_pola,lsepar_contrib,n_Stokes,nb_proc,tab_albedo_pos,lvariable_dust,icell1)
 
-  p_icell = icell_ref
+  p_icell = icell1
 
   !$omp do schedule(static,n_cells/nb_proc)
   do icell=1, n_cells
@@ -750,9 +750,9 @@ subroutine init_dust_source_fct2(lambda,p_lambda,ibin)
   !$omp parallel &
   !$omp default(none) &
   !$omp shared(lambda,n_cells,nang_ray_tracing,eps_dust2,I_sca2,J_th,kappa,kappa_factor,eps_dust2_star,lsepar_pola) &
-  !$omp shared(lsepar_contrib,n_Stokes,nang_ray_tracing_star,nb_proc,tab_albedo_pos,icell_ref,lvariable_dust) &
+  !$omp shared(lsepar_contrib,n_Stokes,nang_ray_tracing_star,nb_proc,tab_albedo_pos,icell1,lvariable_dust) &
   !$omp private(icell,p_icell,dir,iscatt,Q,U,kappa_ext)
-  p_icell = icell_ref
+  p_icell = icell1
   !$omp do schedule(static,n_cells/nb_proc)
   do icell=1, n_cells
      if (lvariable_dust) p_icell = icell
@@ -829,9 +829,9 @@ subroutine calc_Jth(lambda)
         !$omp parallel &
         !$omp default(none) &
         !$omp shared(n_cells,Tdust,wl,lambda,kappa_abs_LTE,kappa_factor,cst_E,J_th) &
-        !$omp shared(lvariable_dust,icell_ref) &
+        !$omp shared(lvariable_dust,icell1) &
         !$omp private(icell,p_icell,Temp,cst_wl,coeff_exp)
-        p_icell = icell_ref
+        p_icell = icell1
         !$omp do
         do icell=1, n_cells
            if (lvariable_dust) p_icell = icell
@@ -1076,7 +1076,7 @@ subroutine calc_Isca_rt2(lambda,p_lambda,ibin)
 
   !$omp parallel &
   !$omp default(none) &
-  !$omp shared(lvariable_dust,Inu,I_sca2,n_cells,tab_s11_pos,uv0,w0,n_Stokes,icell_ref,energie_photon,volume) &
+  !$omp shared(lvariable_dust,Inu,I_sca2,n_cells,tab_s11_pos,uv0,w0,n_Stokes,icell1,energie_photon,volume) &
   !$omp shared(tab_s12_o_s11_pos,tab_s22_o_s11_pos,tab_s33_o_s11_pos,tab_s34_o_s11_pos,tab_s44_o_s11_pos) &
   !$omp shared(lsepar_pola,tab_k,tab_sin_scatt_norm,lambda,p_lambda,n_phi_I,n_theta_I,nang_ray_tracing,lsepar_contrib) &
   !$omp shared(s11_save,tab_cosw,tab_sinw,nb_proc,kappa,kappa_factor,tab_albedo_pos) &
@@ -1098,8 +1098,7 @@ subroutine calc_Isca_rt2(lambda,p_lambda,ibin)
   ROP(4,4) = 1.0_dp
 
   if (.not.lvariable_dust) then   ! we precalculate the s11 as they are all the same
-     icell = icell_ref
-
+     icell = icell1
      do dir=0,1
         do iscatt = 1, nang_ray_tracing
            ! Loop over the specific intensity bins
@@ -1122,7 +1121,7 @@ subroutine calc_Isca_rt2(lambda,p_lambda,ibin)
      enddo ! dir
   endif ! .not.lvariable_dust
 
-  p_icell = icell_ref
+  p_icell = icell1
   !$omp do schedule(static, n_cells/nb_proc)
   do icell = 1, n_cells
      !$ id = omp_get_thread_num() + 1
@@ -1269,7 +1268,7 @@ subroutine calc_Isca_rt2_star(lambda,p_lambda,ibin)
   !$omp parallel &
   !$omp default(none) &
   !$omp shared(n_cells,lambda,p_lambda,ibin,I_spec_star,nang_ray_tracing_star,cos_thet_ray_tracing_star) &
-  !$omp shared(lvariable_dust,r_grid,z_grid,icell_ref,omega_ray_tracing_star,lsepar_pola) &
+  !$omp shared(lvariable_dust,r_grid,z_grid,icell1,omega_ray_tracing_star,lsepar_pola) &
   !$omp shared(tab_s11_pos,tab_s12_o_s11_pos,tab_s22_o_s11_pos,tab_s33_o_s11_pos,tab_s34_o_s11_pos,tab_s44_o_s11_pos) &
   !$omp shared(energie_photon,volume,tab_albedo_pos,kappa,kappa_factor,eps_dust2_star) &
   !$omp private(id,icell,p_icell,stokes,x,y,z,norme,u,v,w,dir,iscatt,cos_scatt,k,omega,cosw,sinw,RPO,ROP,S) &
@@ -1290,7 +1289,7 @@ subroutine calc_Isca_rt2_star(lambda,p_lambda,ibin)
 
   stokes(:) = 0.0_dp
 
-  p_icell = icell_ref
+  p_icell = icell1
 
   !$omp do
   do icell=1, n_cells

src/dust_transfer.f90

@@ -212,8 +212,8 @@ subroutine transfert_poussiere()
      if (loptical_depth_to_cell) call write_optical_depth_to_cell(1)
 
      write(*,*) ""
-     write(*,*) "Dust properties in cell #", icell_ref
-     p_icell = icell_ref
+     write(*,*) "Dust properties in cell #", icell_not_empty
+     p_icell = icell_not_empty
      if (aniso_method==2) write(*,*) "g             ", tab_g_pos(p_icell,1)
      write(*,*) "albedo        ", tab_albedo_pos(p_icell,1)
      if (lsepar_pola.and.(scattering_method == 2)) write(*,*) "polarisability", maxval(-tab_s12_o_s11_pos(:,p_icell,1))
@@ -998,7 +998,7 @@ subroutine propagate_packet(id,lambda,p_lambda,icell,x,y,z,u,v,w,stokes,flag_sta
   if (lvariable_dust) then
      p_icell => icell
   else
-     p_icell => icell_ref
+     p_icell => icell1
   endif
 
   ! Boucle sur les interactions du paquets:

src/gas/atom_transfer.f90

@@ -122,7 +122,7 @@ end subroutine io_write_convergence_maps
 
    subroutine nlte_loop_mali()
    ! ------------------------------------------------------------------------------------ !
-   ! Solve the set of statistical equilibrium equations (SEE) with the 
+   ! Solve the set of statistical equilibrium equations (SEE) with the
    ! Multi-level Accelerated Lambda Iterations method (Rybicki & Hummer 92, Apj 202 209).
    !
    ! By default, the SEE are solved twice.
@@ -150,7 +150,7 @@ subroutine nlte_loop_mali()
       logical :: l_iterate, l_iterate_ne
       integer :: n_xc
       real(kind=dp), dimension(:), pointer :: tab_xc
-      
+
       !Ng's acceleration
       integer, parameter :: Ng_Ndelay_init = 5 !minimal number of iterations before starting the cycle.
                                                !min is 1 (so that conv_speed can be evaluated)
@@ -159,7 +159,7 @@ subroutine nlte_loop_mali()
       real(kind=dp) :: conv_speed_limit
       integer :: iorder, i0_rest, n_iter_accel, iacc
       integer :: Ng_Ndelay, ng_index
-      logical :: lng_turned_on, ng_rest, lconverging, accelerated 
+      logical :: lng_turned_on, ng_rest, lconverging, accelerated
       logical, parameter :: lextrapolate_electron = .false. !extrapolate electrons with populations
       real(kind=dp), dimension(:,:), allocatable :: ngtmp
 
@@ -329,7 +329,7 @@ subroutine nlte_loop_mali()
             ng_index = Neq_ng - mod(n_iter-1,Neq_ng) !overwritten if lng_acceleration.
             ! NOTE :: the index 1 is hard-coded within the non-LTE loop as it stores the actual (running) value
             !           of the populations and electronic density.
-            ! 
+            !
             !                    goes with maxIter
             write(*,'(" *** Iteration #"(1I4)"; step #"(1I1)"; threshold: "(1ES11.2E3)"; Nrays: "(1I5))') &
                      n_iter, etape, precision, n_rayons
@@ -522,7 +522,7 @@ subroutine nlte_loop_mali()
                         !    reshape(ngpop(1:at%Nlevel,nact,:,:),shape=[n_cells,at%Nlevel,Neq_ng],order=[2,1,3]),&!then flatten
                         !    (/n_cells*at%Nlevel,Neq_ng/))
 
-                        call Accelerate(n_cells*at%Nlevel,Ng_Norder,ngtmp) 
+                        call Accelerate(n_cells*at%Nlevel,Ng_Norder,ngtmp)
 
                         !reform in (Nlevel,N_cells,Neq_ng)
                         ngpop(1:at%Nlevel,nact,:,:) = reshape(ngtmp,(/at%Nlevel,n_cells,Neq_ng/))
@@ -1175,7 +1175,7 @@ subroutine atom_line_transfer()
 
          if (lany_init4) then
             call nlte_loop_sobolev()
-            ! MALI step after Sobolev step ? 
+            ! MALI step after Sobolev step ?
             ! if (.not.lescape_prob) then
             !    !to preserve ray-resolution ?
             !    istep_start = 2
@@ -1220,7 +1220,7 @@ subroutine atom_line_transfer()
 
       if (laccretion_shock) then
          !3 + lg(Facc) = lg(Facc) erg/cm2/s
-         if (max_Facc>0) write(*,'("max(lgFacc)="(1F7.3)" W/m^2; min(lgFacc)="(1F7.3)" W/m^2")') & 
+         if (max_Facc>0) write(*,'("max(lgFacc)="(1F7.3)" W/m^2; min(lgFacc)="(1F7.3)" W/m^2")') &
             log10(max_Facc), log10(min_Facc)
          if (max_Tshock>0) write(*,'("max(Tshock)="(1I8)" K; min(Tshock)="(1I8)" K")') &
             nint(max_Tshock), nint(min_Tshock)
@@ -1245,7 +1245,7 @@ subroutine atom_line_transfer()
    end subroutine atom_line_transfer
 
    subroutine init_dust_temperature()
-      !lowering too much the treshold might create some convergence issues in the non-LTE pops or in 
+      !lowering too much the treshold might create some convergence issues in the non-LTE pops or in
       ! the electronic density calculations (0 division mainly for low values).
       real(kind=dp), parameter :: T_formation = 2000.0 ! [K]
       logical, dimension(:), allocatable :: ldust
@@ -1261,7 +1261,7 @@ subroutine init_dust_temperature()
       where(ldust) T(:) = Tdust(:)
       if (any(T < T_formation)) call warning('(atom_transfer) Setting the gas transparent where T < 2000 K.')
       where (T < T_formation) icompute_atomRT = 0
-      !or set the atomic gas temperature to 0 in dust regions ? 
+      !or set the atomic gas temperature to 0 in dust regions ?
       if (any(icompute_atomRT>0)) then
          write(*,*) "T:", real(maxval(T,icompute_atomRT>0)), real(minval(T,icompute_atomRT>0))
          write(*,*) "T (rho_dust = 0):", real(maxval(T,(icompute_atomRT>0).and..not.ldust)), &
@@ -1297,7 +1297,7 @@ subroutine init_dust_atom()
       if (lvariable_dust) then
          p_icell => icell
       else
-         p_icell => icell_ref
+         p_icell => icell1
       endif
 
       call realloc_dust_atom()
@@ -1692,7 +1692,7 @@ subroutine emission_line_tau_surface_map(tau,ibin,iaz)
       do i = 1,npix_x
          !$ id = omp_get_thread_num() + 1
          do j = 1,npix_y
-        
+
             pixelcenter(:,id) = Icorner(:) + (i-0.5_dp) * dx(:) + (j-0.5_dp) * dy(:)
 
             x0(:) = pixelcenter(1,id)