Chemistry Bug Fixes

Author: DimAdam-01

examples/1D_Dilution_Flame/li.yaml

@@ -0,0 +1,239 @@
+description: |-
+  ""
+
+generator: cti2yaml
+cantera-version: 3.1.0
+date: Thu, 10 Apr 2025 09:43:38 -0500
+input-files: [li.cti]
+
+units: {length: cm, quantity: mol, activation-energy: cal/mol}
+
+phases:
+- name: gas
+  thermo: ideal-gas
+  elements: [H, O, N]
+  species: [H, H2, O, OH, H2O, N2, O2, HO2, H2O2]
+  kinetics: gas
+  reactions: all
+  transport: multicomponent
+  state:
+    T: 300.0
+    P: 1.01325e+05
+
+species:
+- name: H
+  composition: {H: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [2.5, 0.0, 0.0, 0.0, 0.0, 2.547163e+04, -0.4601176]
+    - [2.5, 0.0, 0.0, 0.0, 0.0, 2.547163e+04, -0.4601176]
+  transport:
+    model: gas
+    geometry: atom
+    diameter: 2.05
+    well-depth: 145.0
+  note: '120186'
+- name: H2
+  composition: {H: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [3.298124, 8.249442e-04, -8.143015e-07, -9.475434e-11, 4.134872e-13,
+      -1012.521, -3.294094]
+    - [2.991423, 7.000644e-04, -5.633829e-08, -9.231578e-12, 1.582752e-15,
+      -835.034, -1.35511]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 2.92
+    well-depth: 38.0
+    polarizability: 0.79
+    rotational-relaxation: 280.0
+  note: '121286'
+- name: O
+  composition: {O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [2.946429, -1.638166e-03, 2.421032e-06, -1.602843e-09, 3.890696e-13,
+      2.914764e+04, 2.963995]
+    - [2.54206, -2.755062e-05, -3.102803e-09, 4.551067e-12, -4.368052e-16,
+      2.92308e+04, 4.920308]
+  transport:
+    model: gas
+    geometry: atom
+    diameter: 2.75
+    well-depth: 80.0
+  note: '120186'
+- name: OH
+  composition: {H: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 6000.0]
+    data:
+    - [4.12530561, -3.22544939e-03, 6.52764691e-06, -5.79853643e-09, 2.06237379e-12,
+      3346.30913, -0.69043296]
+    - [2.86472886, 1.05650448e-03, -2.59082758e-07, 3.05218674e-11, -1.33195876e-15,
+      3683.62875, 5.70164073]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 2.75
+    well-depth: 80.0
+  note: S9/01
+- name: H2O
+  composition: {H: 2, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [3.386842, 3.474982e-03, -6.354696e-06, 6.968581e-09, -2.506588e-12,
+      -3.020811e+04, 2.590233]
+    - [2.672146, 3.056293e-03, -8.73026e-07, 1.200996e-10, -6.391618e-15,
+      -2.989921e+04, 6.862817]
+  transport:
+    model: gas
+    geometry: nonlinear
+    diameter: 2.605
+    well-depth: 572.4
+    dipole: 1.844
+    rotational-relaxation: 4.0
+  note: '20387'
+- name: N2
+  composition: {N: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [3.298677, 1.40824e-03, -3.963222e-06, 5.641515e-09, -2.444855e-12,
+      -1020.9, 3.950372]
+    - [2.92664, 1.487977e-03, -5.684761e-07, 1.009704e-10, -6.753351e-15,
+      -922.7977, 5.980528]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 3.62
+    well-depth: 97.53
+    polarizability: 1.76
+    rotational-relaxation: 4.0
+  note: '121286'
+- name: O2
+  composition: {O: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [3.212936, 1.127486e-03, -5.75615e-07, 1.313877e-09, -8.768554e-13,
+      -1005.249, 6.034738]
+    - [3.697578, 6.135197e-04, -1.258842e-07, 1.775281e-11, -1.136435e-15,
+      -1233.93, 3.189166]
+  transport:
+    model: gas
+    geometry: linear
+    diameter: 3.458
+    well-depth: 107.4
+    polarizability: 1.6
+    rotational-relaxation: 3.8
+  note: '121386'
+- name: HO2
+  composition: {H: 1, O: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [200.0, 1000.0, 3500.0]
+    data:
+    - [4.30179801, -4.74912051e-03, 2.11582891e-05, -2.42763894e-08, 9.29225124e-12,
+      294.80804, 3.71666245]
+    - [4.0172109, 2.23982013e-03, -6.3365815e-07, 1.1424637e-10, -1.07908535e-14,
+      111.856713, 3.78510215]
+  transport:
+    model: gas
+    geometry: nonlinear
+    diameter: 3.458
+    well-depth: 107.4
+    rotational-relaxation: 1.0
+  note: L5/89
+- name: H2O2
+  composition: {H: 2, O: 2}
+  thermo:
+    model: NASA7
+    temperature-ranges: [300.0, 1000.0, 5000.0]
+    data:
+    - [3.388754, 6.569226e-03, -1.485013e-07, -4.625806e-09, 2.471515e-12,
+      -1.766315e+04, 6.785363]
+    - [4.573167, 4.336136e-03, -1.474689e-06, 2.348904e-10, -1.431654e-14,
+      -1.800696e+04, 0.501137]
+  transport:
+    model: gas
+    geometry: nonlinear
+    diameter: 3.458
+    well-depth: 107.4
+    rotational-relaxation: 3.8
+  note: '120186'
+
+reactions:
+- equation: H + O2 <=> O + OH  # Reaction 1
+  rate-constant: {A: 3.547e+15, b: -0.406, Ea: 1.6599e+04}
+- equation: O + H2 <=> H + OH  # Reaction 2
+  rate-constant: {A: 5.08e+04, b: 2.67, Ea: 6290.0}
+- equation: H2 + OH <=> H2O + H  # Reaction 3
+  rate-constant: {A: 2.16e+08, b: 1.51, Ea: 3430.0}
+- equation: O + H2O <=> OH + OH  # Reaction 4
+  rate-constant: {A: 2.97e+06, b: 2.02, Ea: 1.34e+04}
+- equation: H2 + M <=> H + H + M  # Reaction 5
+  type: three-body
+  rate-constant: {A: 4.577e+19, b: -1.4, Ea: 1.0438e+05}
+  efficiencies: {H2: 2.5, H2O: 12.0}
+- equation: O + O + M <=> O2 + M  # Reaction 6
+  type: three-body
+  rate-constant: {A: 6.165e+15, b: -0.5, Ea: 0.0}
+  efficiencies: {H2: 2.5, H2O: 12.0}
+- equation: O + H + M <=> OH + M  # Reaction 7
+  type: three-body
+  rate-constant: {A: 4.714e+18, b: -1.0, Ea: 0.0}
+  efficiencies: {H2: 2.5, H2O: 12.0}
+- equation: H + OH + M <=> H2O + M  # Reaction 8
+  type: three-body
+  rate-constant: {A: 3.8e+22, b: -2.0, Ea: 0.0}
+  efficiencies: {H2: 2.5, H2O: 12.0}
+- equation: H + O2 (+ M) <=> HO2 (+ M)  # Reaction 9
+  type: falloff
+  low-P-rate-constant: {A: 6.366e+20, b: -1.72, Ea: 524.8}
+  high-P-rate-constant: {A: 1.475e+12, b: 0.6, Ea: 0.0}
+  Troe: {A: 0.8, T3: 1.0e-30, T1: 1.0e+30}
+  efficiencies: {H2: 2.0, H2O: 11.0, O2: 0.78}
+- equation: HO2 + H <=> H2 + O2  # Reaction 10
+  rate-constant: {A: 1.66e+13, b: 0.0, Ea: 823.0}
+- equation: HO2 + H <=> OH + OH  # Reaction 11
+  rate-constant: {A: 7.079e+13, b: 0.0, Ea: 295.0}
+- equation: HO2 + O <=> O2 + OH  # Reaction 12
+  rate-constant: {A: 3.25e+13, b: 0.0, Ea: 0.0}
+- equation: HO2 + OH <=> H2O + O2  # Reaction 13
+  rate-constant: {A: 2.89e+13, b: 0.0, Ea: -497.0}
+- equation: HO2 + HO2 <=> H2O2 + O2  # Reaction 14
+  rate-constant: {A: 4.2e+14, b: 0.0, Ea: 1.1982e+04}
+  duplicate: true
+- equation: HO2 + HO2 <=> H2O2 + O2  # Reaction 15
+  rate-constant: {A: 1.3e+11, b: 0.0, Ea: -1629.3}
+  duplicate: true
+- equation: H2O2 (+ M) <=> OH + OH (+ M)  # Reaction 16
+  type: falloff
+  low-P-rate-constant: {A: 1.202e+17, b: 0.0, Ea: 4.55e+04}
+  high-P-rate-constant: {A: 2.951e+14, b: 0.0, Ea: 4.843e+04}
+  Troe: {A: 0.5, T3: 1.0e-30, T1: 1.0e+30}
+  efficiencies: {H2: 2.5, H2O: 12.0}
+- equation: H2O2 + H <=> H2O + OH  # Reaction 17
+  rate-constant: {A: 2.41e+13, b: 0.0, Ea: 3970.0}
+- equation: H2O2 + H <=> HO2 + H2  # Reaction 18
+  rate-constant: {A: 4.82e+13, b: 0.0, Ea: 7950.0}
+- equation: H2O2 + O <=> OH + HO2  # Reaction 19
+  rate-constant: {A: 9.55e+06, b: 2.0, Ea: 3970.0}
+- equation: H2O2 + OH <=> HO2 + H2O  # Reaction 20
+  rate-constant: {A: 1.0e+12, b: 0.0, Ea: 0.0}
+  duplicate: true
+- equation: H2O2 + OH <=> HO2 + H2O  # Reaction 21
+  rate-constant: {A: 5.8e+14, b: 0.0, Ea: 9557.0}
+  duplicate: true

examples/1D_New_React/README.md

@@ -0,0 +1,14 @@
+# 1D Multi-Component Reactive Shock Tube
+
+References:
+> P. J. Martínez Ferrer, R. Buttay, G. Lehnasch, and A. Mura, “A detailed verification procedure for compressible reactive multicomponent Navier–Stokes solvers”, Comput. & Fluids, vol. 89, pp. 88–110, Jan. 2014. Accessed: Oct. 13, 2024. [Online]. Available: https://doi.org/10.1016/j.compfluid.2013.10.014
+
+> H. Chen, C. Si, Y. Wu, H. Hu, and Y. Zhu, “Numerical investigation of the effect of equivalence ratio on the propagation characteristics and performance of rotating detonation engine”, Int. J. Hydrogen Energy, Mar. 2023. Accessed: Oct. 13, 2024. [Online]. Available: https://doi.org/10.1016/j.ijhydene.2023.03.190
+
+## Initial Condition
+
+<img src="initial.png" height="MAX_HEIGHT"/>
+
+## Results
+
+<img src="result.png" height="MAX_HEIGHT"/>

examples/1D_New_React/case.py

@@ -0,0 +1,117 @@
+#!/usr/bin/env python3
+# References:
+# + https://doi.org/10.1016/j.ijhydene.2023.03.190:  Verification of numerical method
+# + https://doi.org/10.1016/j.compfluid.2013.10.014: 4.7. Multi-species reactive shock tube
+
+import json, argparse
+import cantera as ct
+
+parser = argparse.ArgumentParser(prog="1D_reactive_shocktube", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+parser.add_argument(
+    "--mfc",
+    type=json.loads,
+    default="{}",
+    metavar="DICT",
+    help="MFC's toolchain's internal state.",
+)
+parser.add_argument(
+    "--no-chem",
+    dest="chemistry",
+    default=True,
+    action="store_false",
+    help="Disable chemistry.",
+)
+parser.add_argument("--scale", type=float, default=1, help="Scale.")
+
+args = parser.parse_args()
+
+ctfile = "h2o2.yaml"
+sol_L = ct.Solution(ctfile)
+sol_L.DPX = 0.4214,193138.63 , "H2:2,O2:1,AR:7"
+
+sol_R = ct.Solution(ctfile)
+sol_R.DPX = 0.085, 6670, "H2:2,O2:1,AR:7"
+
+u_l = 0 
+u_r = 0
+
+L = 0.12
+Nx = 1200 * args.scale
+dx = L / Nx
+dt = dx / 1600 * 0.02
+Tend = 100e-6
+
+NT = int(Tend / dt)
+SAVE_COUNT = 100
+NS = NT // SAVE_COUNT
+
+case = {
+    # Logistics
+    "run_time_info": "T",
+    # Computational Domain Parameters
+    "x_domain%beg": 0,
+    "x_domain%end": L,
+    "m": Nx,
+    "n": 0,
+    "p": 0,
+    "dt": float(dt),
+    "t_step_start": 0,
+    "t_step_stop": NT,
+    "t_step_save": 150,
+    "t_step_print": NS,
+    "parallel_io": "F" if args.mfc.get("mpi", True) else "F",
+    # Simulation Algorithm Parameters
+    "model_eqns": 2,
+    "num_fluids": 1,
+    "num_patches": 2,
+    "mpp_lim": "F",
+    "mixture_err": "F",
+    "time_stepper": 3,
+    "weno_order": 5,
+    "weno_eps": 1e-16,
+    "weno_avg": "F",
+    "mapped_weno": "T",
+    "mp_weno": "T",
+    "riemann_solver": 2,
+    "wave_speeds": 1,
+    "avg_state": 2,
+    "bc_x%beg": -2,
+    "bc_x%end": -3,
+    # Chemistry
+    "chemistry": "T" if not args.chemistry else "T",
+    "chem_params%diffusion": "F",
+    "chem_params%reactions": "T",
+    "cantera_file": ctfile,
+    # Formatted Database Files Structure Parameters
+    "format": 1,
+    "precision": 2,
+    "prim_vars_wrt": "T",
+    "chem_wrt_T": "T",
+    "patch_icpp(1)%geometry": 1,
+    "patch_icpp(1)%x_centroid": L / 40,
+    "patch_icpp(1)%length_x": L / 20,
+    "patch_icpp(1)%vel(1)": u_l,
+    "patch_icpp(1)%pres": 6.3*10**5,
+    "patch_icpp(1)%alpha(1)": 1,
+    "patch_icpp(1)%alpha_rho(1)": 0.77,
+      "patch_icpp(2)%geometry": 1,
+    "patch_icpp(2)%x_centroid":  21*L/40,
+    "patch_icpp(2)%length_x": 19*L/20,
+    "patch_icpp(2)%vel(1)": 0,
+    "patch_icpp(2)%pres": sol_R.P,
+    "patch_icpp(2)%alpha(1)": 1,
+    "patch_icpp(2)%alpha_rho(1)": sol_R.density,
+    # Fluids Physical Parameters
+    "fluid_pp(1)%gamma": 1.0e00 / (4.4e00 - 1.0e00),
+    "fluid_pp(1)%pi_inf": 0,
+}
+
+if args.chemistry:
+    for i in range(len(sol_L.Y)):
+        case[f"chem_wrt_Y({i + 1})"] = "T"
+        case[f"patch_icpp(1)%Y({i+1})"] = sol_L.Y[i]
+        case[f"patch_icpp(2)%Y({i+1})"] = sol_R.Y[i]
+
+if __name__ == "__main__":
+    print(json.dumps(case))