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Fix chemistry‑related bugs #829

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Merged
merged 11 commits into from
May 21, 2025
Merged

Fix chemistry‑related bugs #829

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bcaaa35
Chemistry Bug Fixes
DimAdam-01 May 6, 2025
4833d7b
Chemistry Bug Fixes
DimAdam-01 May 6, 2025
c8e7f9f
Format
DimAdam-01 May 6, 2025
652d0fa
Testing-Changes-In-CodeGenerator-For-Pyrometheus
DimAdam-01 May 8, 2025
e63683a
Merge branch 'MFlowCode:master' into my_new_branch
DimAdam-01 May 8, 2025
cc20ee9
Extend Frontier Run Time
DimAdam-01 May 8, 2025
86a5b77
Discard changes to .github/workflows/frontier/submit.sh
sbryngelson May 9, 2025
209dd94
Merge branch 'master' into my_new_branch
sbryngelson May 10, 2025
577a6c0
Pyrometheus library
DimAdam-01 May 18, 2025
76a31f6
Pyrometheus 1.0.3
DimAdam-01 May 19, 2025
e024c03
Pyrometheus 1.0.3 Pypi
DimAdam-01 May 20, 2025
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4 changes: 2 additions & 2 deletions src/common/m_chemistry.fpp
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Expand Up @@ -9,7 +9,7 @@
module m_chemistry

use m_thermochem, only: &
num_species, mol_weights, get_temperature, get_net_production_rates
num_species, molecular_weights, get_temperature, get_net_production_rates

use m_global_parameters

Expand Down Expand Up @@ -91,7 +91,7 @@
!$acc loop seq
do eqn = chemxb, chemxe

omega_m = mol_weights(eqn - chemxb + 1)*omega(eqn - chemxb + 1)
omega_m = molecular_weights(eqn - chemxb + 1)*omega(eqn - chemxb + 1)

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rhs_vf(eqn)%sf(x, y, z) = rhs_vf(eqn)%sf(x, y, z) + omega_m

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2 changes: 1 addition & 1 deletion src/post_process/m_mpi_proxy.fpp
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Expand Up @@ -165,7 +165,7 @@ contains
& 'alt_soundspeed', 'hypoelasticity', 'mhd', 'parallel_io', &
& 'rho_wrt', 'E_wrt', 'pres_wrt', 'gamma_wrt', 'sim_data', &
& 'heat_ratio_wrt', 'pi_inf_wrt', 'pres_inf_wrt', 'cons_vars_wrt', &
& 'prim_vars_wrt', 'c_wrt', 'qm_wrt','schlieren_wrt', &
& 'prim_vars_wrt', 'c_wrt', 'qm_wrt','schlieren_wrt','chem_wrt_T', &
& 'bubbles_euler', 'qbmm', 'polytropic', 'polydisperse', &
& 'file_per_process', 'relax', 'cf_wrt', &
& 'adv_n', 'ib', 'cfl_adap_dt', 'cfl_const_dt', 'cfl_dt', &
Expand Down
3 changes: 3 additions & 0 deletions src/pre_process/m_mpi_proxy.fpp
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Expand Up @@ -128,6 +128,9 @@ contains

call MPI_BCAST(patch_icpp(i)%model_spc, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)

if (chemistry) then
call MPI_BCAST(patch_icpp(i)%Y, size(patch_icpp(i)%Y), mpi_p, 0, MPI_COMM_WORLD, ierr)
end if
! Broadcast IB variables
call MPI_BCAST(patch_ib(i)%geometry, 1, MPI_INTEGER, 0, MPI_COMM_WORLD, ierr)
call MPI_BCAST(patch_ib(i)%model_filepath, len(patch_ib(i)%model_filepath), MPI_CHARACTER, 0, MPI_COMM_WORLD, ierr)
Expand Down
12 changes: 6 additions & 6 deletions src/simulation/include/inline_riemann.fpp
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Expand Up @@ -37,8 +37,8 @@
call get_species_enthalpies_rt(T_L, h_iL)
call get_species_enthalpies_rt(T_R, h_iR)

h_iL = h_iL*gas_constant/mol_weights*T_L
h_iR = h_iR*gas_constant/mol_weights*T_R
h_iL = h_iL*gas_constant/molecular_weights*T_L
h_iR = h_iR*gas_constant/molecular_weights*T_R
call get_species_specific_heats_r(T_L, Cp_iL)
call get_species_specific_heats_r(T_R, Cp_iR)

Expand All @@ -48,17 +48,17 @@

if (abs(T_L - T_R) < eps) then
! Case when T_L and T_R are very close
Cp_avg = sum(Yi_avg(:)*(0.5_wp*Cp_iL(i) + 0.5_wp*Cp_iR(:))*gas_constant/mol_weights(:))
Cv_avg = sum(Yi_avg(:)*((0.5_wp*Cp_iL(i) + 0.5_wp*Cp_iR(:))*gas_constant/mol_weights(:) - gas_constant/mol_weights(:)))
Cp_avg = sum(Yi_avg(:)*(0.5_wp*Cp_iL(:) + 0.5_wp*Cp_iR(:))*gas_constant/molecular_weights(:))
Cv_avg = sum(Yi_avg(:)*((0.5_wp*Cp_iL(:) + 0.5_wp*Cp_iR(:))*gas_constant/molecular_weights(:) - gas_constant/molecular_weights(:)))
else
! Normal calculation when T_L and T_R are sufficiently different
Cp_avg = sum(Yi_avg(:)*(h_iR(:) - h_iL(:))/(T_R - T_L))
Cv_avg = sum(Yi_avg(:)*((h_iR(:) - h_iL(:))/(T_R - T_L) - gas_constant/mol_weights(:)))
Cv_avg = sum(Yi_avg(:)*((h_iR(:) - h_iL(:))/(T_R - T_L) - gas_constant/molecular_weights(:)))
end if

gamma_avg = Cp_avg/Cv_avg

Phi_avg(:) = (gamma_avg - 1._wp)*(vel_avg_rms/2.0_wp - h_avg_2(:)) + gamma_avg*gas_constant/mol_weights(:)*T_avg
Phi_avg(:) = (gamma_avg - 1._wp)*(vel_avg_rms/2.0_wp - h_avg_2(:)) + gamma_avg*gas_constant/molecular_weights(:)*T_avg
c_sum_Yi_Phi = sum(Yi_avg(:)*Phi_avg(:))
end if

Expand Down
12 changes: 6 additions & 6 deletions src/simulation/m_riemann_solvers.fpp
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Expand Up @@ -510,8 +510,8 @@ contains
call get_mixture_molecular_weight(Ys_L, MW_L)
call get_mixture_molecular_weight(Ys_R, MW_R)

Xs_L(:) = Ys_L(:)*MW_L/mol_weights(:)
Xs_R(:) = Ys_R(:)*MW_R/mol_weights(:)
Xs_L(:) = Ys_L(:)*MW_L/molecular_weights(:)
Xs_R(:) = Ys_R(:)*MW_R/molecular_weights(:)

R_gas_L = gas_constant/MW_L
R_gas_R = gas_constant/MW_R
Expand Down Expand Up @@ -1015,8 +1015,8 @@ contains
Y_L = qL_prim_rs${XYZ}$_vf(j, k, l, i)
Y_R = qR_prim_rs${XYZ}$_vf(j + 1, k, l, i)

flux_rs${XYZ}$_vf(j, k, l, i) = (s_M*Y_R*rho_R*vel_R(dir_idx(norm_dir)) &
- s_P*Y_L*rho_L*vel_L(dir_idx(norm_dir)) &
flux_rs${XYZ}$_vf(j, k, l, i) = (s_M*Y_R*rho_R*vel_R(dir_idx(1)) &
- s_P*Y_L*rho_L*vel_L(dir_idx(1)) &
+ s_M*s_P*(Y_L*rho_L - Y_R*rho_R)) &
/(s_M - s_P)
flux_src_rs${XYZ}$_vf(j, k, l, i) = 0._wp
Expand Down Expand Up @@ -2540,8 +2540,8 @@ contains
call get_mixture_molecular_weight(Ys_L, MW_L)
call get_mixture_molecular_weight(Ys_R, MW_R)

Xs_L(:) = Ys_L(:)*MW_L/mol_weights(:)
Xs_R(:) = Ys_R(:)*MW_R/mol_weights(:)
Xs_L(:) = Ys_L(:)*MW_L/molecular_weights(:)
Xs_R(:) = Ys_R(:)*MW_R/molecular_weights(:)

R_gas_L = gas_constant/MW_L
R_gas_R = gas_constant/MW_R
Expand Down
6 changes: 3 additions & 3 deletions toolchain/mfc/run/input.py
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Expand Up @@ -76,10 +76,10 @@ def generate_fpp(self, target) -> None:
# Write the generated Fortran code to the m_thermochem.f90 file with the chosen precision
common.file_write(
os.path.join(modules_dir, "m_thermochem.f90"),
pyro.codegen.fortran90.gen_thermochem_code(
pyro.FortranCodeGenerator().generate(
"m_thermochem",
self.get_cantera_solution(),
module_name="m_thermochem",
real_type=real_type
pyro.CodeGenerationOptions(scalar_type = real_type)
),
True
)
Expand Down
4 changes: 2 additions & 2 deletions toolchain/pyproject.toml
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Expand Up @@ -38,8 +38,8 @@ dependencies = [
"matplotlib",

# Chemistry
"cantera==3.0.1",
"pyrometheus==1.0.2"
"cantera==3.1.0",
"pyrometheus@git+https://github.com/pyrometheus/pyrometheus.git@main"
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@DimAdam-01 I think it would be preferable to reference an official (versioned) release of Pyro instead of referencing the main branch. You can see the original code referenced the 1.0.2 release on Pypi

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@DimAdam-01 i just created a new pyro release 1.0.3 (not sure if it's on pypi just yet)

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I just tested it, it's not on pypi yet: (ERROR: No matching distribution found for pyrometheus==1.0.3)

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yeah i created it 3 min ago

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you can change to pyrometheus==1.0.3 now

]

[tool.hatch.metadata]
Expand Down
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