LowMachReact-Hex Input Configuration Guide

This guide explains how to configure LowMachReact-Hex simulations using the case.nml Fortran namelist file and native mesh input files.

It updates the earlier draft for the current energy/species/Cantera stage. The companion file case_nml_reference.md is the concise option reference. This file is the longer operating guide with recommended modes, examples, validation steps, and common mistakes.

1. Current development assumptions

The current solver should be understood as a constant-density low-Mach/incompressible projection solver with optional species and enthalpy transport.

Important current rules:

1. The pressure projection uses constant flow density rho.
2. Cantera thermodynamic density rho_thermo is diagnostic/future-use only.
3. enable_variable_density = .true. is not supported yet.
4. Energy transport uses sensible enthalpy h as the transported state.
5. Temperature is recovered from h, composition Y, and thermodynamic pressure p0.
6. p0 is currently the uniform operating pressure background_press.
7. Cantera thermodynamics use sensible enthalpy, not raw absolute enthalpy.
8. Option A is the accepted species-energy coupling convention: after species changes composition, preserve transported enthalpy and recover the new temperature.
9. Fixed-temperature species inlets should use boundary composition when evaluating boundary enthalpy.
10. Radiation physics is not coupled yet, but qrad exists as the future volumetric source interface.

2. How the solver reads case.nml

The solver reads named Fortran namelist blocks from the case file. Recommended block order is:

&mesh_input
/

&time_input
/

&fluid_input
/

&solver_input
/

&boundary_input
/

&species_input
/

&energy_input
/

&output_input
/

&profiling_input
/

The order is chosen to match the logical setup sequence: mesh, time, fluid properties, solver controls, boundary conditions, species, energy, output, and profiling.

General Fortran namelist rules:

• Strings should be quoted.
• Logical values are .true. and .false..
• Arrays can be specified as comma-separated lists or with explicit indices.
• Comments begin with !.
• Unknown names in a namelist block should be treated as input errors.

Example indexed species boundary input:

patch_Y(1,1) = 0.0   ! O2 on patch 1
patch_Y(2,1) = 0.0   ! N2 on patch 1
patch_Y(3,1) = 1.0   ! CO2 on patch 1

3. Native mesh input files

mesh_dir points to a directory containing the solver native mesh files.

points.dat

npoints
id x y z
...

cells.dat

ncells
id node1 node2 node3 node4 node5 node6 node7 node8 cx cy cz volume
...

faces.dat

nfaces
id owner neighbor patch nx ny nz area cx cy cz
...

Meaning:

• owner: owner cell id.
• neighbor: neighboring cell id. Boundary faces usually use a boundary/empty neighbor indicator.
• patch: boundary patch id for boundary faces.
• nx ny nz: face normal components.
• area: face area.
• cx cy cz: face centroid.

patches.dat

npatches
id name nfaces
face_id_1 face_id_2 ...
...

Patch names in this file must match patch_name in case.nml.

periodic.dat

Optional file used only for periodic connectivity.

nlinks
face_id pair_face_id neighbor_cell_id
...

4. Fluid configuration

The &fluid_input block controls the flow density, flow viscosity, thermodynamic operating pressure, and Cantera transport refresh interval.

&fluid_input
  rho = 1.0
  nu = 1.0e-2

  enable_cantera = .false.
  enable_variable_density = .false.
  enable_variable_nu = .false.

  cantera_mech_file = "gri30.yaml"
  background_temp = 300.0
  background_press = 101325.0

  transport_update_interval = 10
/

rho: constant flow density

rho is the density used by the flow/projection solver and by the constant-density energy equation.

Current behavior:

flow density = params%rho

This is not replaced by Cantera density. The Cantera density field is diagnostic only.

nu: constant kinematic viscosity

nu is the constant kinematic viscosity used when variable Cantera viscosity is not active.

For fixed-Reynolds-number validation, keep:

enable_variable_nu = .false.

Then the Reynolds number is controlled by:

Re = U_ref L_ref / nu

enable_cantera in fluid_input

This switch controls the Cantera fluid transport path, mainly viscosity. It is independent of species_input enable_cantera.

Recommended current validation setting:

enable_cantera = .false.
enable_variable_nu = .false.

Turn it on only for a dedicated variable-viscosity validation.

enable_variable_density

This is a future variable-density low-Mach flag. Current supported value:

enable_variable_density = .false.

Do not enable it yet. Cantera rho_thermo is available for diagnostics, but the pressure projection still uses constant rho.

enable_variable_nu

This controls whether Cantera viscosity may affect the flow viscosity. If .true., it requires:

enable_cantera = .true.

For current non-reacting scalar validation, the most useful setting is often:

&fluid_input
  enable_cantera = .false.
  enable_variable_nu = .false.
/

&species_input
  enable_cantera = .true.   ! Cantera D_k only
/

This keeps the flow Reynolds number fixed while allowing species diffusivity to vary with T, Y, and p0.

background_temp

Fallback temperature for Cantera transport when energy is disabled.

Current behavior:

if energy is enabled:  Cantera transport uses energy%T
if energy is disabled: Cantera transport uses background_temp

background_press

Uniform thermodynamic pressure used by Cantera.

Current behavior:

p0 = background_press

Cantera uses this pressure for:

• h(T,Y,p0)
• T(h,Y,p0)
• cp(T,Y,p0)
• thermal_conductivity(T,Y,p0)
• rho_thermo(T,Y,p0)
• D_k(T,Y,p0)

Do not confuse this with the hydrodynamic/projection pressure field.

transport_update_interval

Controls how often Cantera transport properties are refreshed.

It controls:

• Cantera mu, if variable viscosity is enabled.
• Cantera species diffusivity D_k, if species Cantera is enabled.

It does not control:

• Energy-side Cantera h <-> T recovery.
• cp refresh.
• Energy-side thermal_conductivity refresh.
• Projection density.
• Pressure projection.

Recommended values:

1       debugging and validation
5-20    faster non-reacting development runs

5. Energy configuration

The &energy_input block controls enthalpy/temperature storage, energy transport, constant-property fallback values, and Cantera thermodynamics.

&energy_input
  enable_energy = .true.
  enable_cantera_thermo = .true.

  thermo_update_interval = 1
  thermo_default_species = "N2"

  initial_T = 300.0
  energy_reference_T = 300.0
  energy_reference_h = 0.0
  energy_cp = 1005.0
  energy_lambda = 0.026
/

enable_energy

Master switch for energy transport.

When enabled, the solver stores and advances:

• T: temperature [K]
• h: transported sensible enthalpy [J/kg]
• qrad: volumetric energy source [W/m^3]
• cp: heat capacity [J/kg/K]
• lambda: thermal conductivity [W/m/K]
• rho_thermo: Cantera diagnostic density [kg/m^3]

Current energy discretization:

energy advection: upwind
energy diffusion: central/two-point gradient of T
source: qrad / rho
integration: explicit

Important: even though h is transported, conduction is driven by grad(T).

enable_cantera_thermo

When .false., the solver uses the constant-cp fallback:

h = h_ref + cp * (T - T_ref)
T = T_ref + (h - h_ref) / cp
lambda = energy_lambda
cp = energy_cp

When .true., the solver uses Cantera thermodynamics:

h_sensible = h_abs(T,Y,p0) - h_abs(T_ref,Y,p0)
T = Cantera_HP_inverse(h_sensible + h_abs(T_ref,Y,p0), Y, p0)
cp = cp(T,Y,p0)
lambda = thermal_conductivity(T,Y,p0)
rho_thermo = rho(T,Y,p0)

Why sensible enthalpy matters:

Cantera absolute enthalpy includes formation/reference contributions. In non-reacting mixing, raw absolute enthalpy can create artificial heat release when composition changes. Using sensible enthalpy relative to the same composition at T_ref removes that artifact.

Cantera thermo sync optimization

During the energy step, the solver may use a combined thermo-sync call:

(T, cp, lambda, rho_thermo) = sync(h, Y, p0)

This is logically equivalent to recovering T from h,Y,p0 and then refreshing cp, lambda, and rho_thermo, but avoids a redundant second Cantera pass.

For species-enabled runs, a pre-flux sync is used after species transport because Y may have changed. For species-disabled runs, the pre-flux sync can be skipped after initialization because the previous post-flux sync remains valid.

Option A: species-energy coupling convention

This is now the accepted convention.

When species transport changes the composition from Y_old to Y_new, preserve transported enthalpy and recover temperature:

h_after_species = h_before_species
T_after_species = T(h_after_species, Y_new, p0)

Do not recompute enthalpy from the old temperature and new composition before energy transport:

Do not use: h = h(T_old, Y_new, p0)

That would preserve temperature instead of the transported energy state and can numerically add or remove sensible enthalpy during passive species mixing.

thermo_update_interval

Reserved for future optimization. Current supported value:

thermo_update_interval = 1

Cantera energy thermodynamics must remain logically synchronized every energy step. The implementation may optimize internally with a combined thermo-sync call and conservative cache, but do not set this above 1 until a stale-thermo strategy is explicitly implemented and validated.

thermo_default_species

Default species for Cantera thermodynamics when species transport is off.

Example:

thermo_default_species = "N2"

Used when:

enable_cantera_thermo = .true.
enable_species = .false.

Ignored when:

enable_species = .true.

In that case, Cantera thermodynamics use transported species%Y.

Useful examples:

thermo_default_species = "N2"
thermo_default_species = "CO2"
thermo_default_species = "H2O"

Use "H2O" with the letter O, not "H20" with zero.

initial_T

Initial gas temperature in Kelvin. Must be positive.

energy_reference_T

Reference temperature used for sensible enthalpy. Must be positive.

Recommended for simple validation:

initial_T = 300.0
energy_reference_T = 300.0

This makes the initial sensible enthalpy close to zero for the initial composition.

energy_reference_h

Reference enthalpy for constant-cp mode. Usually:

energy_reference_h = 0.0

energy_cp

Constant heat capacity for non-Cantera energy mode. Must be positive.

energy_lambda

Constant thermal conductivity for non-Cantera energy mode. Must be non-negative.

For visible diffusion debugging, you may temporarily use a larger value than air's physical value.

6. Species configuration

The &species_input block controls passive species transport, fallback diffusivity, Cantera species diffusivity, and future reactions.

&species_input
  enable_species = .true.
  enable_reactions = .false.
  enable_cantera = .true.

  nspecies = 3
  species_name = "O2", "N2", "CO2"

  initial_Y = 0.0, 1.0, 0.0
  species_diffusivity = 2.0e-5, 2.0e-5, 2.0e-5
/

enable_species

Master switch for species transport.

enable_reactions

Future reaction chemistry switch. Current validation setting:

enable_reactions = .false.

Do not turn reactions on until passive species, passive energy, and Cantera thermo have been validated.

enable_cantera in species_input

This controls Cantera species diffusivity D_k.

When .false.:

D_k = species_diffusivity(k)

When .true.:

D_k = Cantera mixture-averaged diffusivity D_k(T,Y,p0)

The temperature source is:

energy enabled:  energy%T
energy disabled: background_temp

nspecies

Number of transported species. Must be non-negative and within the compiled max_species limit.

species_name

Transported species names. These must match species in the Cantera mechanism whenever Cantera species transport or Cantera thermodynamics with transported species is enabled.

Example:

species_name = "O2", "N2", "CO2"

initial_Y

Initial domain mass fractions.

Examples:

initial_Y = 0.0, 1.0, 0.0   ! pure N2 for O2,N2,CO2 list
initial_Y = 0.0, 0.0, 1.0   ! pure CO2 for O2,N2,CO2 list

species_diffusivity

Fallback constant diffusivity values [m^2/s]. Used when species_input enable_cantera = .false..

7. Boundary configuration

Boundary configuration links the physical boundary names in patches.dat to flow, pressure, species, and temperature conditions.

Example:

&boundary_input
  n_patches = 5
  patch_name = "inlet", "outlet", "wall", "zmin", "zmax"

  patch_type = "dirichlet", "neumann", "wall", "symmetric", "symmetric"

  patch_velocity_type = "fixed_value", "zero_gradient", "no_slip", "symmetric", "symmetric"
  patch_pressure_type = "zero_gradient", "zero_gradient", "zero_gradient", "zero_gradient", "zero_gradient"
  patch_temperature_type = "fixed_value", "zero_gradient", "zero_gradient", "zero_gradient", "zero_gradient"
  patch_species_type = "fixed_value", "zero_gradient", "zero_gradient", "zero_gradient", "zero_gradient"

  patch_u = 1.0, 0.0, 0.0, 0.0, 0.0
  patch_v = 0.0, 0.0, 0.0, 0.0, 0.0
  patch_w = 0.0, 0.0, 0.0, 0.0, 0.0

  patch_p = 0.0, 0.0, 0.0, 0.0, 0.0
  patch_dpdn = 0.0, 0.0, 0.0, 0.0, 0.0

  patch_T = 400.0, 300.0, 300.0, 300.0, 300.0

  patch_Y(1,1) = 0.0
  patch_Y(2,1) = 0.0
  patch_Y(3,1) = 1.0
/

Boundary type aliases

The parser recognizes these aliases:

Velocity boundaries

• Wall/no-slip uses the configured wall velocity.
• Symmetry removes the normal velocity component.
• Zero-gradient and periodic use extrapolated/effective neighbor behavior.

Pressure boundaries

Use fixed pressure only where needed to anchor the pressure field. Otherwise use zero-gradient for typical outlets/walls, depending on the case design.

Temperature boundaries

Use:

patch_temperature_type = "fixed_value"
patch_T = ...

for fixed-temperature inlets or hot/cold walls.

If a patch has:

patch_temperature_type = "zero_gradient"

then patch_T is not used as a fixed value on that patch.

Species boundaries

Use:

patch_species_type = "fixed_value"
patch_Y(k,patch) = ...

for species inlets.

Mass fractions should sum to about 1 on fixed-value species patches.

Fixed-temperature inlet with species composition

For Cantera thermo plus transported species, a fixed-temperature species inlet should be interpreted as:

T_b = patch_T(patch)
Y_b = patch_Y(:,patch)
h_b = h(T_b,Y_b,p0)

This is important for hot/cold fuel/oxidizer inlets. It avoids evaluating boundary enthalpy with interior composition or a default bath gas.

8. Output configuration

&output_input
  output_dir = "cases/rectangle_2D/output"
  write_vtu = .true.
  write_diagnostics = .true.
/

output_dir

Directory for generated output files.

Before rerunning after changing output arrays, remove old output:

rm -rf cases/rectangle_2D/output

write_vtu

Controls VTU/PVTU/PVD visualization output.

write_diagnostics

Controls CSV diagnostics. Current diagnostic files may include:

• diagnostics.csv
• energy_diagnostics.csv

9. Profiling configuration

&profiling_input
  enable_profiling = .true.
  nested_profiling = .true.
/

enable_profiling

Enable MPI-aware profiling.

nested_profiling

Show a nested call tree in the terminal profiling report.

Current profiling region names include:

Transport_Update
Projection_Step
Species_Transport
Energy_Transport
Diagnostics_Write_Flow
Diagnostics_Write_Energy
Output_Write_VTU

For Cantera thermo energy runs, nested energy children may include:

Energy_Cantera_PreSync
Energy_PreFlux_Exchange
Energy_Flux_Update
Energy_Cantera_PostSync
Energy_Final_Exchange

The profiler reports inclusive wall time. Flat rows are not additive when nested timers are enabled.

10. Recommended configuration modes

Mode 1: Baseline hydrodynamics

Use this to verify that energy/species additions did not change old flow behavior.

&fluid_input
  rho = 1.0
  nu = 1.0e-2
  enable_cantera = .false.
  enable_variable_density = .false.
  enable_variable_nu = .false.
  cantera_mech_file = "gri30.yaml"
  background_temp = 300.0
  background_press = 101325.0
  transport_update_interval = 10
/

&species_input
  enable_species = .false.
  enable_reactions = .false.
  enable_cantera = .false.
  nspecies = 0
/

&energy_input
  enable_energy = .false.
  enable_cantera_thermo = .false.
  thermo_update_interval = 1
  thermo_default_species = "N2"
  initial_T = 300.0
  energy_reference_T = 300.0
  energy_reference_h = 0.0
  energy_cp = 1005.0
  energy_lambda = 0.026
/

Expected result:

• Old flow diagnostics remain unchanged within numerical tolerance.
• No energy fields are required.

Mode 2: Constant-property energy

Use this to validate energy numerics without Cantera complexity.

&energy_input
  enable_energy = .true.
  enable_cantera_thermo = .false.
  thermo_update_interval = 1
  thermo_default_species = "N2"
  initial_T = 300.0
  energy_reference_T = 300.0
  energy_reference_h = 0.0
  energy_cp = 1005.0
  energy_lambda = 0.026
/

Expected result:

• Uniform temperature remains uniform.
• Pure diffusion is smooth and stable under explicit timestep limits.
• qrad remains zero unless a source is prescribed later.

Mode 3: Cantera thermodynamics without transported species

Use this for Stage 2A thermo smoke tests.

&species_input
  enable_species = .false.
  enable_reactions = .false.
  enable_cantera = .false.
  nspecies = 0
/

&energy_input
  enable_energy = .true.
  enable_cantera_thermo = .true.
  thermo_update_interval = 1
  thermo_default_species = "N2"
  initial_T = 300.0
  energy_reference_T = 300.0
  energy_reference_h = 0.0
  energy_cp = 1005.0
  energy_lambda = 0.026
/

Change thermo_default_species from "N2" to "CO2" to verify that cp, thermal_conductivity, rho_thermo, and thermal diffusivity respond to the selected gas.

Mode 4: Cantera thermodynamics with transported species

Use this for Stage 2B non-reacting species/energy coupling.

&species_input
  enable_species = .true.
  enable_reactions = .false.
  enable_cantera = .false.
  nspecies = 3
  species_name = "O2", "N2", "CO2"
  initial_Y = 0.0, 1.0, 0.0
  species_diffusivity = 2.0e-5, 2.0e-5, 2.0e-5
/

&energy_input
  enable_energy = .true.
  enable_cantera_thermo = .true.
  thermo_update_interval = 1
  thermo_default_species = "N2"
  initial_T = 300.0
  energy_reference_T = 300.0
  energy_reference_h = 0.0
  energy_cp = 1005.0
  energy_lambda = 0.026
/

In this mode:

thermo_default_species is ignored
Cantera thermo uses transported species%Y
h is preserved through species changes
T is recovered from h,Y,p0

Mode 5: Cantera species diffusivity with fixed-Re flow

Use this to test variable D_k while keeping the flow Reynolds number fixed.

&fluid_input
  rho = 1.0
  nu = 1.0e-2
  enable_cantera = .false.
  enable_variable_density = .false.
  enable_variable_nu = .false.
  cantera_mech_file = "gri30.yaml"
  background_temp = 300.0
  background_press = 101325.0
  transport_update_interval = 10
/

&species_input
  enable_species = .true.
  enable_reactions = .false.
  enable_cantera = .true.
  nspecies = 3
  species_name = "O2", "N2", "CO2"
  initial_Y = 0.0, 1.0, 0.0
  species_diffusivity = 2.0e-5, 2.0e-5, 2.0e-5
/

Expected result:

D_k = Cantera D_k(T,Y,p0)
nu = constant
rho = constant
Re = fixed

Mode 6: Non-reacting counterflow development target

Use this only after simpler tests pass.

Recommended rules:

• enable_species = .true.
• enable_reactions = .false.
• enable_energy = .true.
• enable_cantera_thermo = .true.
• enable_variable_density = .false.
• enable_variable_nu = .false. initially
• Fixed-temperature/fixed-species inlets use matching patch_T and patch_Y
• Use Option A enthalpy/species coupling

Expected result:

• Non-reacting mixing layer trends are plausible.
• Temperature remains physical and bounded.
• sum_Y remains close to 1.
• Exact agreement with fully variable-density counterflow is not expected yet.

11. ParaView and VTU fields

Depending on enabled physics, ParaView may show the following arrays.

Flow fields

• velocity
• pressure

pressure is hydrodynamic/projection pressure, not thermodynamic pressure.

Energy fields

• temperature
• enthalpy
• qrad
• cp
• thermal_conductivity
• rho_thermo
• thermal_diffusivity
• thermo_pressure

Meanings:

Species fields

Examples:

• Y_O2
• Y_N2
• Y_CO2
• sum_Y
• D_O2
• D_N2
• D_CO2

D_<species> is the diffusivity used by species transport.

If arrays are missing in ParaView after adding new output fields, remove old output and rerun:

rm -rf cases/rectangle_2D/output
make rectangle_2D-release NP=8

Then inspect the output metadata:

grep -R "thermal_diffusivity|thermo_pressure\|D_" cases/rectangle_2D/output

12. Runtime terminal reporting

The solver should print a mode summary similar to:

Flow density mode: constant rho = ... kg/m^3
Flow viscosity mode: constant nu = ... m^2/s
Cantera rho_thermo: diagnostic only, not used by projection
Cantera transport update interval: N step(s) [mu/D_k only]
Cantera transport temperature source: energy%T
Cantera thermo update interval: every energy step
Cantera thermo sync: combined T/cp/lambda/rho_thermo from h,Y,p0
Cantera thermodynamic pressure p0: ... Pa

Use this block to verify that the active runtime mode matches the intended validation mode.

13. Recommended validation ladder

Step 1: Energy disabled regression

Run an existing flow-only or flow/species case with:

enable_energy = .false.

Expected:

• Old flow/species behavior is unchanged.
• Build and output still work.

Step 2: Constant-property energy initialization

Use:

enable_energy = .true.
enable_cantera_thermo = .false.

Expected:

• temperature is initialized to initial_T.
• enthalpy follows constant-cp formula.
• qrad = 0.

Step 3: Constant-property diffusion

Use zero velocity and fixed hot/cold temperature boundaries.

Expected:

• Temperature evolves smoothly.
• Steady profile is reasonable for the geometry.
• Explicit timestep is stable.

Step 4: Cantera h/T roundtrip without species

Use:

enable_cantera_thermo = .true.
enable_species = .false.

Expected:

• h(T) followed by T(h) recovers the original temperature.
• Changing thermo_default_species changes thermodynamic properties.

Step 5: Cantera thermo with species, no reactions

Use:

enable_species = .true.
enable_reactions = .false.
enable_cantera_thermo = .true.

Expected:

• Thermodynamic properties follow transported composition.
• Enthalpy is preserved through species updates using Option A.
• Temperature remains bounded during passive mixing.

Step 6: Cantera species diffusivity with fixed-Re flow

Use species Cantera only:

&fluid_input
  enable_cantera = .false.
  enable_variable_nu = .false.
/

&species_input
  enable_cantera = .true.
/

Expected:

• D_k varies with T, Y, and p0.
• Flow viscosity remains fixed.

Step 7: Non-reacting counterflow

Use opposed inlets, species boundary compositions, fixed inlet temperatures, and reactions off.

Compare:

• Centerline temperature.
• Centerline species profiles.
• Mixture fraction trend.
• Stagnation-plane location.
• Scalar dissipation trend.

Expected:

• Qualitative non-reacting mixing-layer behavior.
• No expectation of exact variable-density Cantera 1D agreement until variable-density low-Mach coupling is implemented.

Step 8: Manufactured qrad tests, future

Before external radiation physics, test prescribed qrad patterns:

• Uniform heating.
• Uniform cooling.
• Gaussian heating/cooling.
• Localized source.

Expected:

• Positive qrad heats the gas.
• Negative qrad cools the gas.
• Domain-integrated energy change matches integrated qrad.

14. Common mistakes

Mistake 1: Enabling variable density too early

Do not use:

enable_variable_density = .true.

Current solver does not implement variable-density projection. Use rho_thermo only as a diagnostic field.

Mistake 2: Turning on all Cantera switches at once

Avoid starting with:

fluid_input enable_cantera = .true.
species_input enable_cantera = .true.
enable_cantera_thermo = .true.
enable_variable_nu = .true.

Instead, validate one feature at a time.

Mistake 3: Confusing the two enable_cantera switches

There are two separate blocks:

&fluid_input
  enable_cantera = ...   ! flow viscosity path
/

&species_input
  enable_cantera = ...   ! species diffusivity path
/

Use the species switch for Cantera D_k. Use the fluid switch only when testing Cantera viscosity.

Mistake 4: Using projection pressure as thermodynamic pressure

Current thermodynamic pressure is:

background_press = 101325.0

The pressure field written to output is projection pressure, not Cantera thermodynamic pressure.

Mistake 5: Fixed temperature with missing temperature type

Setting patch_T alone is not enough. You also need:

patch_temperature_type = "fixed_value"

for that patch.

Mistake 6: Species inlet mass fractions not summing to 1

For fixed species inlets, check:

sum_k patch_Y(k,patch) ~= 1

This is especially important for Cantera thermo and species diffusivity.

Mistake 7: Using interior composition for inlet enthalpy

For fixed-temperature species inlets, the intended rule is:

h_b = h(T_b,Y_b,p0)

not:

h_b = h(T_b,Y_interior,p0)

Mistake 8: Recomputing enthalpy after species transport

The accepted Option A convention is:

preserve h
recover T from h,Y_new,p0

Do not preserve old temperature by recomputing h(T_old,Y_new,p0).

Mistake 9: Expecting exact counterflow agreement too early

The current flow solver remains constant-density. Exact agreement with variable-density 1D Cantera counterflow is not expected yet.

Mistake 10: Reusing old ParaView output after changing arrays

Remove output when array structure changes:

rm -rf cases/<case>/output

Then rerun the case.

15. Suggested documentation set in the repo

Recommended files:

docs/case_nml_reference.md
docs/input_configuration_guide.md
docs/energy_thermo_conventions.md
docs/enthalpy_species_coupling_convention.md
docs/validation_ladder.md

This file can serve as docs/input_configuration_guide.md. The compact companion file can serve as docs/case_nml_reference.md.