fix(post): exchange the chemistry q_T seam ghosts for EVERY chemistry run (post converts over the ghost shell; the diffusion-only condition left rank-seam Newton guesses uninitialized -> NaN T/pres/c, first exposed by the 2-rank chemistry AMR case); seed q_T over the interior in the simulation's order

Author: sbryngelson

src/common/m_mpi_common.fpp

@@ -570,7 +570,10 @@ contains
             chem_T_comm = .true.
             v_size = nVar + 1
 #else
-        else if (present(q_T_sf) .and. chemistry .and. chem_params%diffusion) then
+        else if (present(q_T_sf) .and. chemistry) then
+            ! post_process converts cons->prim over the ghost-inclusive bounds, so the temperature
+            ! Newton guess must be valid at rank seams for EVERY chemistry run (not only diffusion):
+            ! an unexchanged seam ghost is an uninitialized guess -> NaN T/pres/c in the output
             chem_T_comm = .true.
             v_size = nVar + 1
 #endif

src/post_process/m_start_up.fpp

@@ -156,7 +156,11 @@ contains
 
         if (amr) call s_read_amr_data(t_step)
 
-        if (chemistry) call s_compute_q_T_sf(q_T_sf, q_cons_vf, idwbuff)
+        ! seed the chemistry temperature over the INTERIOR only (mirrors the simulation,
+        ! m_start_up): the ghost q_cons is unread at this point, so a ghost-inclusive sweep
+        ! would Newton-iterate on garbage (NaN under NaN-init builds) at rank seams and
+        ! physical boundaries; s_populate_variables_buffers below extends q_T into the ghosts
+        if (chemistry) call s_compute_q_T_sf(q_T_sf, q_cons_vf, idwint)
 
         if (buff_size > 0) then
             call s_populate_grid_variables_buffers()