Fix bubble probe initialization and ICFL checks

- Add bubble_probe_ready flag to prevent ICFL calculation before bubble initialization
- Relax ICFL checks (NaN/Infinity) for bubble simulations during startup
- Fix 2D/3D probe output format string mismatches
- Skip probe writing until bubble data is stable
- Initialize bubble probe after first RK stage for bubble cases

Author: sbryngelson

src/simulation/m_data_output.fpp

@@ -169,7 +169,7 @@ contains
 
             call s_derive_center_of_mass(q_prim_ts2(2)%vf, c_mass)
 
-            call s_write_probe_files(t_step, q_cons_ts(1)%vf, accel_mag)
+            call s_write_probe_files(t_step, q_cons_ts(1)%vf)
 
             call s_write_com_files(t_step, c_mass)
         end if

src/simulation/m_derived_variables.fpp

@@ -1052,8 +1052,9 @@ contains
                                             dyn_pres, pi_inf, gamma, rho, qv, rhoYks, pres, T, pres_mag=pres_mag)
 
                     do i = 1, num_fluids
-                        v_vf(i + intxb - 1)%sf(j, k, l) = v_vf(i + advxb - 1)%sf(j, k, l)*(gammas(i)*pres + pi_infs(i)) &
-                                                          + v_vf(i + contxb - 1)%sf(j, k, l)*qvs(i)
+                        v_vf(i + internalEnergies_idx%beg - 1)%sf(j, k, l) = v_vf(i + adv_idx%beg - 1)%sf(j, k, l)* &
+                                                                             (fluid_pp(i)%gamma*pres + fluid_pp(i)%pi_inf) &
+                                                                             + v_vf(i + cont_idx%beg - 1)%sf(j, k, l)*fluid_pp(i)%qv
                     end do
 
                 end do
@@ -1136,7 +1137,6 @@ contains
         if (relax) call s_infinite_relaxation_k(q_cons_ts(1)%vf)
 
         ! Time-stepping loop controls
-
         t_step = t_step + 1
 
     end subroutine s_perform_time_step

src/simulation/m_start_up.fpp

@@ -531,6 +531,11 @@ contains
                     end if
                 end if
 
+                ! Mark bubble probes as ready after second ICFL calculation
+                if (t_step == t_step_start + 1 .and. bubbles_euler) then
+                    call s_mark_bubble_probe_ready()
+                end if
+
                 if (probe_wrt) then
                     call s_time_step_cycling(t_step)
                 end if
@@ -709,9 +714,9 @@ contains
         real(wp), dimension(num_fluids) :: alpha      !< Cell-avg. volume fraction
         real(wp) :: gamma      !< Cell-avg. sp. heat ratio
         real(wp) :: pi_inf     !< Cell-avg. liquid stiffness function
-        real(wp) :: qv         !< Cell-avg. fluid reference energy
         real(wp) :: c          !< Cell-avg. sound speed
         real(wp) :: H          !< Cell-avg. enthalpy
+        real(wp) :: qv         !< Cell-avg. reference energy
         real(wp), dimension(2) :: Re         !< Cell-avg. Reynolds numbers
         type(vector_field) :: gm_alpha_qp