docs: update index variable references to eqn_idx struct (#1365) (#1371)

Author: sbryngelson

.claude/rules/common-pitfalls.md

@@ -13,13 +13,15 @@
 
 ## Field Variable Indexing
 - Conserved variables: `q_cons_vf(1:sys_size)`. Primitive: `q_prim_vf(1:sys_size)`.
-- Index ranges depend on `model_eqns` and enabled features (set in `m_global_parameters.fpp`):
-  - `cont_idx` — continuity (partial densities, one per fluid)
-  - `mom_idx` — momentum components
-  - `E_idx` — total energy (scalar)
-  - `adv_idx` — volume fractions (advection equations)
-  - `bub_idx`, `stress_idx`, `xi_idx`, `species_idx`, `B_idx`, `c_idx` — optional
-- Shorthand scalars: `momxb`/`momxe`, `contxb`/`contxe`, `advxb`/`advxe`, etc.
+- All equation indices live in the unified `eqn_idx` struct (`eqn_idx_info` type in `m_derived_types.fpp`).
+  Index ranges depend on `model_eqns` and enabled features (set in `m_global_parameters.fpp`):
+  - `eqn_idx%cont` — continuity range (partial densities, one per fluid)
+  - `eqn_idx%mom` — momentum range
+  - `eqn_idx%E` — total energy (scalar)
+  - `eqn_idx%adv` — volume fractions (advection equations)
+  - `eqn_idx%bub`, `eqn_idx%stress`, `eqn_idx%xi`, `eqn_idx%species`, `eqn_idx%B` — optional
+  - `eqn_idx%gamma`, `eqn_idx%pi_inf`, `eqn_idx%alf`, `eqn_idx%int_en` — additional scalars/ranges
+- Use `eqn_idx%cont%beg`/`eqn_idx%cont%end`, `eqn_idx%mom%beg`/`eqn_idx%mom%end`, etc. (old `contxb`/`contxe`, `momxb`/`momxe` shorthands are gone)
 - `sys_size` = total number of conserved variables (computed at startup)
 - Changing `model_eqns` or enabling features changes ALL index positions
 

docs/documentation/architecture.md.in

@@ -49,8 +49,8 @@ The index layout within `q_cons_vf` depends on the flow model:
 ```
 For model_eqns == 2 (5-equation, multi-fluid):
 
-  Index:    1 .. num_fluids | num_fluids+1 .. +num_vels | E_idx | adv_idx
-  Meaning:  alpha*rho_k     | momentum components       | energy | volume fractions
+  Index:    1 .. num_fluids | num_fluids+1 .. +num_vels | eqn_idx%E | eqn_idx%adv
+  Meaning:  alpha*rho_k     | momentum components       | energy    | volume fractions
 ```
 
 Additional variables are appended for bubbles, elastic stress, magnetic fields, or chemistry species when those models are enabled. The total count is `sys_size`.

docs/documentation/case.md

@@ -235,7 +235,7 @@ In the example above, the following code is generated:
 
 ```f90
 if (patch_id == 2) then
-    q_prim_vf(contxb)%sf(i, 0, 0) = 1 + 0.1*sin(20*x_cc(i)*3.141592653589793)
+    q_prim_vf(eqn_idx%cont%beg)%sf(i, 0, 0) = 1 + 0.1*sin(20*x_cc(i)*3.141592653589793)
 end if
 ```
 

docs/documentation/contributing.md

@@ -334,7 +334,7 @@ do l = 0, p
     do k = 0, n
         do j = 0, m
             rho = q_prim_vf(1)%sf(j, k, l)
-            pres = q_prim_vf(E_idx)%sf(j, k, l)
+            pres = q_prim_vf(eqn_idx%E)%sf(j, k, l)
             ! ... use rho, pres as thread-local ...
         end do
     end do
@@ -369,7 +369,7 @@ do l = 0, p
         do j = 0, m
             $:GPU_LOOP(parallelism='[seq]')
             do i = 1, num_fluids
-                alpha(i) = q_prim_vf(advxb + i - 1)%sf(j, k, l)
+                alpha(i) = q_prim_vf(eqn_idx%adv%beg + i - 1)%sf(j, k, l)
             end do
         end do
     end do