From af2c7213f3ebb68d464301e924b70df7fa4bd769 Mon Sep 17 00:00:00 2001
From: Grzegorz Kowal <grzegorz@amuncode.org>
Date: Mon, 4 Feb 2019 14:43:10 -0200
Subject: [PATCH] COORDINATES: Use ncells instead of in, jn, and kn.

Also rename ng to nghosts.

Signed-off-by: Grzegorz Kowal <grzegorz@amuncode.org>
---
 sources/boundaries.F90  | 140 ++++++++++++++++++----------------------
 sources/coordinates.F90 |  91 ++++++++++++--------------
 sources/equations.F90   |   4 +-
 sources/integrals.F90   |   8 ++-
 sources/io.F90          |  73 +++++++++++----------
 sources/mesh.F90        |  30 ++++-----
 6 files changed, 163 insertions(+), 183 deletions(-)

diff --git a/sources/boundaries.F90 b/sources/boundaries.F90
index 2d7e293..e542cec 100644
--- a/sources/boundaries.F90
+++ b/sources/boundaries.F90
@@ -555,7 +555,7 @@ module boundaries
 #endif /* MPI */
     use blocks         , only : ndims, nsides
     use coordinates    , only : minlev, maxlev
-    use coordinates    , only : in, jn, kn
+    use coordinates    , only : ni => ncells
     use coordinates    , only : ib, ie, ibl
     use coordinates    , only : jb, je, jbl
     use coordinates    , only : kb, ke, kbl
@@ -607,15 +607,15 @@ module boundaries
 
 ! calculate half sizes
 !
-    ih = in / 2
-    jh = jn / 2
+    ih = ni / 2
+    jh = ni / 2
 #if NDIMS == 2
-    kh = kn
+    kh = 1
     kl = 1
-    ku = kn
+    ku = 1
 #endif /* NDIMS == 2 */
 #if NDIMS == 3
-    kh = kn / 2
+    kh = ni / 2
 #endif /* NDIMS == 3 */
 
 #ifdef MPI
@@ -1331,8 +1331,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : ni => ncells, ng => nghosts
     use coordinates    , only : im , jm , km
     use coordinates    , only : faces_gc, faces_dc
     use equations      , only : nv
@@ -1385,9 +1384,9 @@ module boundaries
 
 ! calculate half sizes
 !
-    ih = in / 2
-    jh = jn / 2
-    kh = kn / 2
+    ih = ni / 2
+    jh = ni / 2
+    kh = ni / 2
 
 #ifdef MPI
 ! prepare the block exchange structures
@@ -1708,8 +1707,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : ni => ncells, ng => nghosts
     use coordinates    , only : im , jm , km
     use coordinates    , only : faces_gr
     use equations      , only : nv
@@ -1760,9 +1758,9 @@ module boundaries
 
 ! calculate half sizes
 !
-    ih = in / 2
-    jh = jn / 2
-    kh = kn / 2
+    ih = ni / 2
+    jh = ni / 2
+    kh = ni / 2
 
 #ifdef MPI
 ! prepare the block exchange structures
@@ -2074,8 +2072,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : ni => ncells, ng => nghosts
     use coordinates    , only : im , jm , km
     use coordinates    , only : faces_gp
     use equations      , only : nv
@@ -2127,9 +2124,9 @@ module boundaries
 
 ! calculate the sizes
 !
-    ih = in + ng
-    jh = jn + ng
-    kh = kn + ng
+    ih = ni + ng
+    jh = ni + ng
+    kh = ni + ng
 
 #ifdef MPI
 ! prepare the block exchange structures
@@ -2505,8 +2502,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
-    use coordinates    , only : in, jn, kn
+    use coordinates    , only : ni => ncells, ng => nghosts
     use coordinates    , only : im, jm, km
     use coordinates    , only : edges_gc, edges_dc
     use equations      , only : nv
@@ -2559,10 +2555,10 @@ module boundaries
 
 ! calculate half sizes
 !
-    ih = in / 2
-    jh = jn / 2
+    ih = ni / 2
+    jh = ni / 2
 #if NDIMS == 3
-    kh = kn / 2
+    kh = ni / 2
 #endif /* NDIMS == 3 */
 
 #ifdef MPI
@@ -2967,8 +2963,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : ni => ncells, ng => nghosts
     use coordinates    , only : im , jm , km
     use coordinates    , only : edges_gr
     use equations      , only : nv
@@ -3019,10 +3014,10 @@ module boundaries
 
 ! calculate half sizes
 !
-    ih = in / 2
-    jh = jn / 2
+    ih = ni / 2
+    jh = ni / 2
 #if NDIMS == 3
-    kh = kn / 2
+    kh = ni / 2
 #endif /* NDIMS == 3 */
 
 #ifdef MPI
@@ -3410,8 +3405,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : ni => ncells, ng => nghosts
     use coordinates    , only : im , jm , km
     use coordinates    , only : edges_gp
     use equations      , only : nv
@@ -3463,10 +3457,10 @@ module boundaries
 
 ! calculate the sizes
 !
-    ih = in + ng
-    jh = jn + ng
+    ih = ni + ng
+    jh = ni + ng
 #if NDIMS == 3
-    kh = kn + ng
+    kh = ni + ng
 #endif /* NDIMS == 3 */
 
 #ifdef MPI
@@ -3925,7 +3919,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
+    use coordinates    , only : ng => nghosts
     use coordinates    , only : im, jm, km
     use coordinates    , only : corners_gc, corners_dc
     use equations      , only : nv
@@ -4323,7 +4317,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
+    use coordinates    , only : ng => nghosts
     use coordinates    , only : im , jm , km
     use coordinates    , only : corners_gr
     use equations      , only : nv
@@ -4696,7 +4690,7 @@ module boundaries
     use blocks         , only : block_meta, block_data, block_leaf
     use blocks         , only : list_meta, list_leaf
     use blocks         , only : block_info, pointer_info
-    use coordinates    , only : ng
+    use coordinates    , only : ng => nghosts
     use coordinates    , only : im , jm , km
     use coordinates    , only : corners_gp
     use equations      , only : nv
@@ -5078,7 +5072,7 @@ module boundaries
 
 ! import external procedures and variables
 !
-    use coordinates    , only : im , jm , km , ng
+    use coordinates    , only : im , jm , km , ng => nghosts
     use coordinates    , only : ib , jb , kb , ie , je , ke
     use coordinates    , only : ibl, jbl, kbl, ieu, jeu, keu
     use equations      , only : nv
@@ -5691,9 +5685,7 @@ module boundaries
 
 ! import external procedures and variables
 !
-    use coordinates    , only : ng, nd
-    use coordinates    , only : in
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : ni => ncells, ng => nghosts, nd
     use coordinates    , only : im , jm , km
     use coordinates    , only : faces_dr
     use equations      , only : nv
@@ -5736,8 +5728,8 @@ module boundaries
 
 ! calculate half sizes
 !
-      jh = jn / 2
-      kh = kn / 2
+      jh = ni / 2
+      kh = ni / 2
 
 ! restrict the face region to the output array
 !
@@ -5755,8 +5747,8 @@ module boundaries
 
 ! calculate half sizes
 !
-      ih = in / 2
-      kh = kn / 2
+      ih = ni / 2
+      kh = ni / 2
 
 ! restrict the face region to the output array
 !
@@ -5774,8 +5766,8 @@ module boundaries
 
 ! calculate half sizes
 !
-      ih = in / 2
-      jh = jn / 2
+      ih = ni / 2
+      jh = ni / 2
 
 ! restrict the face region to the output array
 !
@@ -5816,9 +5808,7 @@ module boundaries
 
 ! import external procedures and variables
 !
-    use coordinates    , only : ng, nh
-    use coordinates    , only : in
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : nh
     use coordinates    , only : im , jm , km
     use coordinates    , only : faces_dp
     use equations      , only : nv, idn, ipr
@@ -5973,9 +5963,7 @@ module boundaries
 
 ! import external procedures and variables
 !
-    use coordinates    , only : ng, nd
-    use coordinates    , only : in
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : ni => ncells, ng => nghosts, nd
     use coordinates    , only : im , jm , km
     use coordinates    , only : edges_dr
     use equations      , only : nv
@@ -6028,7 +6016,7 @@ module boundaries
 
 ! calculate half size
 !
-      ih = in / 2
+      ih = ni / 2
 
 ! restrict the edge region to the output array
 !
@@ -6055,7 +6043,7 @@ module boundaries
 
 ! calculate half size
 !
-      jh = jn / 2
+      jh = ni / 2
 
 ! restrict the edge region to the output array
 !
@@ -6083,7 +6071,7 @@ module boundaries
 
 ! calculate half size
 !
-      kh = kn / 2
+      kh = ni / 2
 
 ! restrict the edge region to the output array
 !
@@ -6125,9 +6113,7 @@ module boundaries
 
 ! import external procedures and variables
 !
-    use coordinates    , only : ng, nh
-    use coordinates    , only : in
-    use coordinates    , only : in , jn , kn
+    use coordinates    , only : nh
     use coordinates    , only : im , jm , km
     use coordinates    , only : edges_dp
     use equations      , only : nv, idn, ipr
@@ -6310,7 +6296,7 @@ module boundaries
 
 ! import external procedures and variables
 !
-    use coordinates    , only : ng, nd
+    use coordinates    , only : ng => nghosts, nd
     use coordinates    , only : im , jm , km
     use coordinates    , only : corners_dr
     use equations      , only : nv
@@ -6405,7 +6391,7 @@ module boundaries
 
 ! import external procedures and variables
 !
-    use coordinates    , only : ng, nh
+    use coordinates    , only : ng => nghosts, nh
     use coordinates    , only : im , jm , km
     use coordinates    , only : corners_dp
     use equations      , only : nv, idn, ipr
@@ -6594,7 +6580,7 @@ module boundaries
 ! import external procedures and variables
 !
     use blocks         , only : block_data
-    use coordinates    , only : in, jn, kn
+    use coordinates    , only : ni => ncells
     use equations      , only : nv
 
 ! local variables are not implicit by default
@@ -6621,13 +6607,13 @@ module boundaries
 #if NDIMS == 2
 ! average fluxes from higher level neighbor
 !
-      fb(1:nv,:,:) = (fn(1:nv,1:jn:2,1:kn) + fn(1:nv,2:jn:2,1:kn)) / 2.0d+00
+      fb(1:nv,:,:) = (fn(1:nv,1:ni:2, :  ) + fn(1:nv,2:ni:2, :  )) / 2.0d+00
 #endif /* NDIMS == 2 */
 #if NDIMS == 3
 ! average fluxes from higher level neighbor
 !
-      fb(1:nv,:,:) = ((fn(1:nv,1:in:2,1:kn:2) + fn(1:nv,2:in:2,2:kn:2))        &
-                    + (fn(1:nv,1:in:2,2:kn:2) + fn(1:nv,2:in:2,1:kn:2)))       &
+      fb(1:nv,:,:) = ((fn(1:nv,1:ni:2,1:ni:2) + fn(1:nv,2:ni:2,2:ni:2))        &
+                    + (fn(1:nv,1:ni:2,2:ni:2) + fn(1:nv,2:ni:2,1:ni:2)))       &
                     / 4.0d+00
 #endif /* NDIMS == 3 */
 
@@ -6638,13 +6624,13 @@ module boundaries
 #if NDIMS == 2
 ! average fluxes from higher level neighbor
 !
-      fb(1:nv,:,:) = (fn(1:nv,1:in:2,1:kn) + fn(1:nv,2:in:2,1:kn)) / 2.0d+00
+      fb(1:nv,:,:) = (fn(1:nv,1:ni:2, :  ) + fn(1:nv,2:ni:2, :  )) / 2.0d+00
 #endif /* NDIMS == 2 */
 #if NDIMS == 3
 ! average fluxes from higher level neighbor
 !
-      fb(1:nv,:,:) = ((fn(1:nv,1:in:2,1:kn:2) + fn(1:nv,2:in:2,2:kn:2))        &
-                    + (fn(1:nv,1:in:2,2:kn:2) + fn(1:nv,2:in:2,1:kn:2)))       &
+      fb(1:nv,:,:) = ((fn(1:nv,1:ni:2,1:ni:2) + fn(1:nv,2:ni:2,2:ni:2))        &
+                    + (fn(1:nv,1:ni:2,2:ni:2) + fn(1:nv,2:ni:2,1:ni:2)))       &
                     / 4.0d+00
 #endif /* NDIMS == 3 */
 
@@ -6655,8 +6641,8 @@ module boundaries
 
 ! average fluxes from higher level neighbor
 !
-      fb(1:nv,:,:) = ((fn(1:nv,1:in:2,1:jn:2) + fn(1:nv,2:in:2,2:jn:2))        &
-                    + (fn(1:nv,1:in:2,2:jn:2) + fn(1:nv,2:in:2,1:jn:2)))       &
+      fb(1:nv,:,:) = ((fn(1:nv,1:ni:2,1:ni:2) + fn(1:nv,2:ni:2,2:ni:2))        &
+                    + (fn(1:nv,1:ni:2,2:ni:2) + fn(1:nv,2:ni:2,1:ni:2)))       &
                     / 4.0d+00
 #endif /* NDIMS == 3 */
 
@@ -6688,7 +6674,7 @@ module boundaries
 ! include external variables
 !
     use blocks        , only : block_data, list_data
-    use coordinates   , only : im , jm , km , in , jn , kn
+    use coordinates   , only : ni => ncells, im , jm , km
     use coordinates   , only : ib , jb , kb , ie , je , ke
     use coordinates   , only : ibl, jbl, kbl, ieu, jeu, keu
     use equations     , only : nv
@@ -6741,13 +6727,13 @@ module boundaries
 ! update remaining left layers of the X boundary
 !
         do i = 1, ibl
-          call prim2cons(jn, pdata%q(1:nv,i,jb:je,k), pdata%u(1:nv,i,jb:je,k))
+          call prim2cons(ni, pdata%q(1:nv,i,jb:je,k), pdata%u(1:nv,i,jb:je,k))
         end do ! i = 1, ibl
 
 ! update remaining right layers of the X boundary
 !
         do i = ieu, im
-          call prim2cons(jn, pdata%q(1:nv,i,jb:je,k), pdata%u(1:nv,i,jb:je,k))
+          call prim2cons(ni, pdata%q(1:nv,i,jb:je,k), pdata%u(1:nv,i,jb:je,k))
         end do ! i = 1, ibl
 
       end do ! k = 1, km
@@ -6760,13 +6746,13 @@ module boundaries
 ! update the remaining front layers of the Z boundary
 !
         do k = 1, kbl
-          call prim2cons(in, pdata%q(1:nv,ib:ie,j,k), pdata%u(1:nv,ib:ie,j,k))
+          call prim2cons(ni, pdata%q(1:nv,ib:ie,j,k), pdata%u(1:nv,ib:ie,j,k))
         end do ! k = 1, kbl
 
 ! update the remaining back layers of the Z boundary
 !
         do k = keu, km
-          call prim2cons(in, pdata%q(1:nv,ib:ie,j,k), pdata%u(1:nv,ib:ie,j,k))
+          call prim2cons(ni, pdata%q(1:nv,ib:ie,j,k), pdata%u(1:nv,ib:ie,j,k))
         end do ! k = keu, km
 
       end do ! j = jb, je
diff --git a/sources/coordinates.F90 b/sources/coordinates.F90
index 48a3525..bc805be 100644
--- a/sources/coordinates.F90
+++ b/sources/coordinates.F90
@@ -37,13 +37,13 @@ module coordinates
 ! MODULE PARAMETERS:
 ! =================
 !
-! the domain block dimensions
+! the number of interior cells along each block dimension
 !
-  integer     , save :: nc =  8, in =  8, jn =  8, kn =  1
+  integer     , save :: ncells  = 8
 
-! the number of ghost zones
+! the number of ghost zones at each side of the block
 !
-  integer     , save :: ng =  2, nh =  1, nd =  4
+  integer     , save :: nghosts = 2, nh =  1, nd =  4
 
 ! the domain block dimensions including the ghost zones
 !
@@ -152,8 +152,8 @@ module coordinates
 !
 !   Arguments:
 !
-!     ncells   - the number of cells per dimension in a block;
-!     nghosts  - the number of ghosts cells at each side in a block;
+!     ni       - the number of interior cells per dimension in a block;
+!     ng       - the number of ghosts cells at each side in a block;
 !     tlevel   - the maximum refinement level for coordinate generation;
 !     bdims    - the base level dimension in blocks;
 !     xmn, xmx, ymn, ymx, zmn, zmx -
@@ -163,7 +163,7 @@ module coordinates
 !
 !===============================================================================
 !
-  subroutine initialize_coordinates(ncells, nghosts, tlevel, bdims,            &
+  subroutine initialize_coordinates(ni, ng, tlevel, bdims,                     &
                                   xmn, xmx, ymn, ymx, zmn, zmx, verbose, iret)
 
 ! include external procedures
@@ -177,7 +177,7 @@ module coordinates
 ! subroutine arguments
 !
     logical              , intent(in)    :: verbose
-    integer              , intent(in)    :: ncells, nghosts, tlevel
+    integer              , intent(in)    :: ni, ng, tlevel
     integer, dimension(3), intent(in)    :: bdims
     real(kind=8)         , intent(in)    :: xmn, xmx, ymn, ymx, zmn, zmx
     integer              , intent(inout) :: iret
@@ -185,9 +185,9 @@ module coordinates
 ! local variables
 !
     character(len=32) :: lbndry, ubndry
-    integer           :: i, j, k, l, p, q, r, ff
+    integer           :: i, j, k, l, p, q, r
     integer           :: fi, fj, fk
-    integer           :: ni, nj, nk, nm, np, nr, nq, ns, nt, nu
+    integer           :: nn, nm, np, nr, nq, ns, nt, nu
     logical           :: info
 !
 !-------------------------------------------------------------------------------
@@ -195,16 +195,8 @@ module coordinates
 ! set the number of cells along each block dimension and
 ! the number of ghost zones
 !
-    nc = ncells
-    ng = nghosts
-
-! set the block dimensions
-!
-    in = nc
-    jn = nc
-#if NDIMS == 3
-    kn = nc
-#endif /* NDIMS == 3 */
+    ncells  = ni
+    nghosts = ng
 
 ! calculate half and double of the number of ghose zones
 !
@@ -213,10 +205,10 @@ module coordinates
 
 ! calculate the block dimensions including ghost cells
 !
-    im = in + 2 * ng
-    jm = jn + 2 * ng
+    im = ni + 2 * ng
+    jm = ni + 2 * ng
 #if NDIMS == 3
-    km = kn + 2 * ng
+    km = ni + 2 * ng
 #endif /* NDIMS == 3 */
 
 ! prepare indices
@@ -231,14 +223,14 @@ module coordinates
 !
     ih  = im / 2
     ib  = ng +  1
-    ie  = ng + in
+    ie  = ng + ni
     ibl = ib - 1
     ibu = ib + ng - 1
     iel = ie - ng + 1
     ieu = ie + 1
     jh  = jm / 2
     jb  = ng +  1
-    je  = ng + jn
+    je  = ng + ni
     jbl = jb - 1
     jbu = jb + ng - 1
     jel = je - ng + 1
@@ -246,7 +238,7 @@ module coordinates
 #if NDIMS == 3
     kh  = km / 2
     kb  = ng +  1
-    ke  = ng + kn
+    ke  = ng + ni
     kbl = kb - 1
     kbu = kb + ng - 1
     kel = ke - ng + 1
@@ -350,17 +342,14 @@ module coordinates
 
 ! calculate the block resolution at each level
 !
-      ff      = 2**(l - 1)
-      ni      = in * ff
-      nj      = jn * ff
-      nk      = kn * ff
+      nn      = ni * 2**(l - 1)
 
 ! calculate the cell sizes for each level
 !
-      adx (l) = xlen / (domain_base_dims(1) * ni)
-      ady (l) = ylen / (domain_base_dims(2) * nj)
+      adx (l) = xlen / (domain_base_dims(1) * nn)
+      ady (l) = ylen / (domain_base_dims(2) * nn)
 #if NDIMS == 3
-      adz (l) = zlen / (domain_base_dims(3) * nk)
+      adz (l) = zlen / (domain_base_dims(3) * nn)
 #endif /* NDIMS == 3 */
 #if NDIMS == 2
       adr (l) = sqrt(adx(l)**2 + ady(l)**2)
@@ -393,11 +382,11 @@ module coordinates
 
 ! initialize ghost subarray indices
 !
-    np = nc + ng
-    nm = nc - ng
-    nr = nc - nd
-    nq = nc - nh
-    ns = nc / 2
+    np = ni + ng
+    nm = ni - ng
+    nr = ni - nd
+    nq = ni - nh
+    ns = ni / 2
     nt = np / 2
     nu = nm / 2
 #if NDIMS == 2
@@ -441,8 +430,8 @@ module coordinates
         edges_gr(i,j,1)%u(:) = edges_gr(i,j,1)%l(:) + (/ ns, ng /) - 1
         edges_gr(i,j,2)%u(:) = edges_gr(i,j,2)%l(:) + (/ ng, ns /) - 1
 
-        edges_dr(i,q,1)%u(:) = edges_dr(i,q,1)%l(:) + (/ nc, nd /) - 1
-        edges_dr(p,j,2)%u(:) = edges_dr(p,j,2)%l(:) + (/ nd, nc /) - 1
+        edges_dr(i,q,1)%u(:) = edges_dr(i,q,1)%l(:) + (/ ni, nd /) - 1
+        edges_dr(p,j,2)%u(:) = edges_dr(p,j,2)%l(:) + (/ nd, ni /) - 1
 
 ! for edge prolongation
 !
@@ -568,9 +557,9 @@ module coordinates
           faces_gr(i,j,k,2)%u(:) = faces_gr(i,j,k,2)%l(:) + (/ ns, ng, ns /) - 1
           faces_gr(i,j,k,3)%u(:) = faces_gr(i,j,k,3)%l(:) + (/ ns, ns, ng /) - 1
 
-          faces_dr(p,j,k,1)%u(:) = faces_dr(p,j,k,1)%l(:) + (/ nd, nc, nc /) - 1
-          faces_dr(i,q,k,2)%u(:) = faces_dr(i,q,k,2)%l(:) + (/ nc, nd, nc /) - 1
-          faces_dr(i,j,r,3)%u(:) = faces_dr(i,j,r,3)%l(:) + (/ nc, nc, nd /) - 1
+          faces_dr(p,j,k,1)%u(:) = faces_dr(p,j,k,1)%l(:) + (/ nd, ni, ni /) - 1
+          faces_dr(i,q,k,2)%u(:) = faces_dr(i,q,k,2)%l(:) + (/ ni, nd, ni /) - 1
+          faces_dr(i,j,r,3)%u(:) = faces_dr(i,j,r,3)%l(:) + (/ ni, ni, nd /) - 1
 
 ! for face prolongation
 !
@@ -658,9 +647,9 @@ module coordinates
           edges_gr(i,j,k,2)%u(:) = edges_gr(i,j,k,2)%l(:) + (/ ng, ns, ng /) - 1
           edges_gr(i,j,k,3)%u(:) = edges_gr(i,j,k,3)%l(:) + (/ ng, ng, ns /) - 1
 
-          edges_dr(i,q,r,1)%u(:) = edges_dr(i,q,r,1)%l(:) + (/ nc, nd, nd /) - 1
-          edges_dr(p,j,r,2)%u(:) = edges_dr(p,j,r,2)%l(:) + (/ nd, nc, nd /) - 1
-          edges_dr(p,q,k,3)%u(:) = edges_dr(p,q,k,3)%l(:) + (/ nd, nd, nc /) - 1
+          edges_dr(i,q,r,1)%u(:) = edges_dr(i,q,r,1)%l(:) + (/ ni, nd, nd /) - 1
+          edges_dr(p,j,r,2)%u(:) = edges_dr(p,j,r,2)%l(:) + (/ nd, ni, nd /) - 1
+          edges_dr(p,q,k,3)%u(:) = edges_dr(p,q,k,3)%l(:) + (/ nd, nd, ni /) - 1
 
 ! for edge prolongation
 !
@@ -831,13 +820,13 @@ module coordinates
 !
       bm(:) = domain_base_dims(:)
       rm(:) = bm(:) * 2**(maxlev - 1)
-      cm(:) = bm(:) * nc
-      fm(:) = rm(:) * nc
+      cm(:) = bm(:) * ncells
+      fm(:) = rm(:) * ncells
 
       call print_section(verbose, "Geometry")
-      call print_parameter(verbose, "refinement to level"  , maxlev)
-      call print_parameter(verbose, "number of block cells", nc    )
-      call print_parameter(verbose, "number of ghost zones", ng    )
+      call print_parameter(verbose, "refinement to level"  , maxlev )
+      call print_parameter(verbose, "number of block cells", ncells )
+      call print_parameter(verbose, "number of ghost zones", nghosts)
       write(msg,"(i0)") maxval(fm(1:NDIMS))
       p = len(trim(adjustl(msg)))
       write(msg,"(i0)") maxval(rm(1:NDIMS))
diff --git a/sources/equations.F90 b/sources/equations.F90
index ab76e09..24b57b0 100644
--- a/sources/equations.F90
+++ b/sources/equations.F90
@@ -1150,7 +1150,7 @@ module equations
 
 ! include external procedures and variables
 !
-    use coordinates, only : im , jm , km , in , jn , kn
+    use coordinates, only : ncells, im , jm , km
     use coordinates, only : ib , jb , kb , ie , je , ke
     use coordinates, only : ibl, jbl, kbl, ieu, jeu, keu
 
@@ -1176,7 +1176,7 @@ module equations
 
 ! convert conserved variables to primitive ones
 !
-        call cons2prim(in, uu(1:nv,ib:ie,j,k), qq(1:nv,ib:ie,j,k))
+        call cons2prim(ncells, uu(1:nv,ib:ie,j,k), qq(1:nv,ib:ie,j,k))
 
       end do ! j = jb, je
     end do ! k = kb, ke
diff --git a/sources/integrals.F90 b/sources/integrals.F90
index c0cf031..5acc1e0 100644
--- a/sources/integrals.F90
+++ b/sources/integrals.F90
@@ -256,7 +256,7 @@ module integrals
 ! import external variables and subroutines
 !
     use blocks         , only : block_meta, block_data, list_data
-    use coordinates    , only : in, jn, kn, ib, jb, kb, ie, je, ke
+    use coordinates    , only : ni => ncells, ib, jb, kb, ie, je, ke
     use coordinates    , only : advol, voli
     use equations      , only : idn, ipr, ivx, ivy, ivz, ibx, iby, ibz, ibp
     use equations      , only : ien, imx, imy, imz
@@ -289,7 +289,11 @@ module integrals
 ! local arrays
 !
     real(kind=8), dimension(narr)     :: inarr, avarr, mnarr, mxarr
-    real(kind=8), dimension(in,jn,kn) :: vel, mag, sqd, tmp
+#if NDIMS == 3
+    real(kind=8), dimension(ni,ni,ni) :: vel, mag, sqd, tmp
+#else /* NDIMS == 3 */
+    real(kind=8), dimension(ni,ni, 1) :: vel, mag, sqd, tmp
+#endif /* NDIMS == 3 */
 
 ! parameters
 !
diff --git a/sources/io.F90 b/sources/io.F90
index 1fbe6bf..97bbbaf 100644
--- a/sources/io.F90
+++ b/sources/io.F90
@@ -1773,7 +1773,7 @@ module io
     use blocks         , only : get_mblocks, get_dblocks, get_nleafs
     use blocks         , only : get_last_id
     use coordinates    , only : minlev, maxlev
-    use coordinates    , only : nc, ng, in, jn, kn
+    use coordinates    , only : ncells, nghosts
     use coordinates    , only : ddims => domain_base_dims
     use coordinates    , only : xmin, xmax, ymin, ymax, zmin, zmax
     use coordinates    , only : periodic
@@ -1801,6 +1801,7 @@ module io
 
 ! local vectors
 !
+    integer, dimension(3)         :: bdims = 1
     integer, dimension(3)         :: per
 
 ! local allocatable arrays
@@ -1854,8 +1855,8 @@ module io
     call write_attribute(gid, 'mblocks' , get_mblocks())
     call write_attribute(gid, 'dblocks' , get_dblocks())
     call write_attribute(gid, 'nleafs'  , get_nleafs() )
-    call write_attribute(gid, 'ncells'  , nc           )
-    call write_attribute(gid, 'nghosts' , ng           )
+    call write_attribute(gid, 'ncells'  , ncells       )
+    call write_attribute(gid, 'nghosts' , nghosts      )
     call write_attribute(gid, 'minlev'  , minlev       )
     call write_attribute(gid, 'maxlev'  , maxlev       )
     call write_attribute(gid, 'nprocs'  , nprocs       )
@@ -1885,7 +1886,8 @@ module io
 
 ! store the vector attributes
 !
-    call write_attribute(gid, 'dims' , (/ in, jn, kn /))
+    bdims(1:NDIMS) = ncells
+    call write_attribute(gid, 'dims'            , bdims)
     call write_attribute(gid, 'domain_base_dims', ddims)
 
 ! store random number generator seed values
@@ -1951,7 +1953,7 @@ module io
     use blocks         , only : append_metablock
     use blocks         , only : set_last_id, get_last_id
     use blocks         , only : get_mblocks, get_dblocks, get_nleafs
-    use coordinates    , only : nc, ng, in, jn, kn
+    use coordinates    , only : ncells, nghosts
     use coordinates    , only : xmin, xmax, ymin, ymax, zmin, zmax
     use evolution      , only : step, time, dt, dtn
     use hdf5           , only : hid_t, hsize_t
@@ -2037,14 +2039,14 @@ module io
 
 ! check the block dimensions
 !
-    if (lncells /= nc) then
+    if (lncells /= ncells) then
       write(error_unit,"('[',a,']: ',a)") trim(loc)                            &
                       , "The block dimensions do not match!"
     end if
 
 ! check the number of ghost layers
 !
-    if (lnghost /= ng) then
+    if (lnghost /= nghosts) then
       write(error_unit,"('[',a,']: ',a)") trim(loc)                            &
                       , "The number of ghost layers does not match!"
     end if
@@ -3303,7 +3305,7 @@ module io
 !
     use blocks         , only : block_data, list_data
     use blocks         , only : get_dblocks
-    use coordinates    , only : im, jm, km, in, jn, kn
+    use coordinates    , only : ni => ncells, im, jm, km
     use coordinates    , only : ib, jb, kb, ie, je, ke
     use equations      , only : nv, pvars
     use hdf5           , only : hid_t, hsize_t
@@ -3321,7 +3323,7 @@ module io
 ! HDF5 variables
 !
     integer(hid_t)             :: gid
-    integer(hsize_t)           :: dm(4)
+    integer(hsize_t)           :: dm(4) = 1
 
 ! local variables
 !
@@ -3371,9 +3373,11 @@ module io
           ju    = jm
           ku    = km
         else
-          dm(2) = in
-          dm(3) = jn
-          dm(4) = kn
+          dm(2) = ni
+          dm(3) = ni
+#if NDIMS == 3
+          dm(4) = ni
+#endif /* NDIMS == 3 */
 
           il    = ib
           jl    = jb
@@ -3479,7 +3483,7 @@ module io
 !
     use blocks         , only : block_data, list_data
     use blocks         , only : get_dblocks
-    use coordinates    , only : im, jm, km, in, jn, kn
+    use coordinates    , only : ni => ncells, im, jm, km
     use coordinates    , only : ib, jb, kb, ie, je, ke
     use equations      , only : nv, cvars
     use hdf5           , only : hid_t, hsize_t
@@ -3497,7 +3501,7 @@ module io
 ! HDF5 variables
 !
     integer(hid_t)             :: gid
-    integer(hsize_t)           :: dm(4)
+    integer(hsize_t)           :: dm(4) = 1
 
 ! local variables
 !
@@ -3547,9 +3551,11 @@ module io
           ju    = jm
           ku    = km
         else
-          dm(2) = in
-          dm(3) = jn
-          dm(4) = kn
+          dm(2) = ni
+          dm(3) = ni
+#if NDIMS == 3
+          dm(4) = ni
+#endif /* NDIMS == 3 */
 
           il    = ib
           jl    = jb
@@ -7174,9 +7180,8 @@ module io
     use blocks         , only : get_dblocks
     use equations      , only : nv, pvars
     use mpitools       , only : nproc
-    use coordinates    , only : in, jn, kn
+    use coordinates    , only : ni => ncells, ng => nghosts
     use coordinates    , only : adx, ady, adz
-    use coordinates    , only : ng
     use evolution      , only : time
 
 ! local variables are not implicit by default
@@ -7232,27 +7237,27 @@ module io
 
 ! prepare dimensions
 !
-      ip = in + 1
-      jp = jn + 1
+      ip = ni + 1
+      jp = ni + 1
 #if NDIMS == 3
-      kp = kn + 1
+      kp = ni + 1
 #endif /* NDIMS == 3 */
 
 #if NDIMS == 3
-      write(stmp, "(1i8)") kn
-      write(ttmp, "(1i8)") jn
+      write(stmp, "(1i8)") ni
+      write(ttmp, "(1i8)") ni
       stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
-      write(ttmp, "(1i8)") in
+      write(ttmp, "(1i8)") ni
 #else /* NDIMS == 3 */
-      write(stmp, "(1i8)") jn
-      write(ttmp, "(1i8)") in
+      write(stmp, "(1i8)") ni
+      write(ttmp, "(1i8)") ni
 #endif /* NDIMS == 3 */
       bdim = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
 
-      write(stmp, "(1i8)") kn
-      write(ttmp, "(1i8)") jn
+      write(stmp, "(1i8)") ni
+      write(ttmp, "(1i8)") ni
       stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
-      write(ttmp, "(1i8)") in
+      write(ttmp, "(1i8)") ni
       stmp = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
       write(ttmp, "(1i8)") get_dblocks()
       sdim = trim(adjustl(stmp)) // ' ' // trim(adjustl(ttmp))
@@ -7261,15 +7266,15 @@ module io
 !
 #if NDIMS == 3
       if (with_ghosts) then
-        slab(:) = (/ ng, ng, ng, -1, 1, 1, 1, 1, kn, jn, in, 1 /)
+        slab(:) = (/ ng, ng, ng, -1, 1, 1, 1, 1, ni, ni, ni, 1 /)
       else
-        slab(:) = (/  0,  0,  0, -1, 1, 1, 1, 1, kn, jn, in, 1 /)
+        slab(:) = (/  0,  0,  0, -1, 1, 1, 1, 1, ni, ni, ni, 1 /)
       end if
 #else /* NDIMS == 3 */
       if (with_ghosts) then
-        slab(:) = (/  0, ng, ng, -1, 1, 1, 1, 1,  1, jn, in, 1 /)
+        slab(:) = (/  0, ng, ng, -1, 1, 1, 1, 1,  1, ni, ni, 1 /)
       else
-        slab(:) = (/  0,  0,  0, -1, 1, 1, 1, 1,  1, jn, in, 1 /)
+        slab(:) = (/  0,  0,  0, -1, 1, 1, 1, 1,  1, ni, ni, 1 /)
       end if
 #endif /* NDIMS == 3 */
 
diff --git a/sources/mesh.F90 b/sources/mesh.F90
index e2e2820..e277443 100644
--- a/sources/mesh.F90
+++ b/sources/mesh.F90
@@ -261,7 +261,7 @@ module mesh
     use blocks         , only : ndims
     use blocks         , only : get_mblocks, get_nleafs
     use coordinates    , only : ddims => domain_base_dims
-    use coordinates    , only : ng, nd, in, jn, kn, im, jm, km
+    use coordinates    , only : ni => ncells, ng => nghosts, nd, im, jm, km
     use coordinates    , only : toplev
     use mpitools       , only : master, nprocs
 
@@ -338,10 +338,10 @@ module mesh
 !
           ff  = 2**(toplev - 1)
           fcv = 1.0d+00 / n
-          fef = 1.0d+00 * (ddims(1) * in * ff + nd) / im
-          fef =     fef * (ddims(2) * jn * ff + nd) / jm
+          fef = 1.0d+00 * (ddims(1) * ni * ff + nd) / im
+          fef =     fef * (ddims(2) * ni * ff + nd) / jm
 #if NDIMS == 3
-          fef =     fef * (ddims(3) * kn * ff + nd) / km
+          fef =     fef * (ddims(3) * ni * ff + nd) / km
 #endif /* NDIMS == 3 */
 
 ! reset the first execution flag
@@ -1034,7 +1034,7 @@ module mesh
 ! import external procedures and variables
 !
     use blocks         , only : block_meta, block_data, nchildren
-    use coordinates    , only : ng, nh, in, jn, kn, im, jm, km
+    use coordinates    , only : ncells, nghosts, nh, im, jm, km
     use coordinates    , only : ib, ie, jb, je, kb, ke
     use equations      , only : nv, idn, ien
     use interpolations , only : limiter_prol
@@ -1062,7 +1062,7 @@ module mesh
 
 ! local arrays
 !
-    integer     , dimension(3)     :: dm
+    integer     , dimension(3)     :: dm = 1
     real(kind=8), dimension(NDIMS) :: du
 
 ! local allocatable arrays
@@ -1087,10 +1087,7 @@ module mesh
 
 ! prepare dimensions
 !
-    dm(:) = 2 * ((/ in, jn, kn /) + ng)
-#if NDIMS == 2
-    dm(3) = 1
-#endif /* NDIMS == 2 */
+    dm(1:NDIMS) = 2 * (ncells + nghosts)
 
 ! allocate array for the expanded arrays
 !
@@ -1203,10 +1200,10 @@ module mesh
 
 ! calculate indices of the current child subdomain
 !
-      il = 1 + ic * in
-      jl = 1 + jc * jn
+      il = 1 + ic * ncells
+      jl = 1 + jc * ncells
 #if NDIMS == 3
-      kl = 1 + kc * kn
+      kl = 1 + kc * ncells
 #endif /* NDIMS == 3 */
 
       iu = il + im - 1
@@ -1260,9 +1257,8 @@ module mesh
 
 ! import external procedures and variables
 !
-    use blocks         , only : ndims
     use blocks         , only : block_meta, block_data, nchildren
-    use coordinates    , only : ng, nh, in, jn, kn, im, jm, km
+    use coordinates    , only : nh, im, jm, km
     use coordinates    , only : ih, jh, kh, ib, jb, kb, ie, je, ke
     use equations      , only : nv
 
@@ -1282,7 +1278,7 @@ module mesh
 
 ! local arrays
 !
-    integer, dimension(ndims) :: pos
+    integer, dimension(NDIMS) :: pos
 
 ! local pointers
 !
@@ -1310,7 +1306,7 @@ module mesh
 
 ! obtain the child position in the parent block
 !
-      pos(1:ndims) = pchild%meta%pos(1:ndims)
+      pos(1:NDIMS) = pchild%meta%pos(1:NDIMS)
 
 ! calculate the bound indices of the source nad destination arrays
 !