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Examples

T3 ships with several example input files in the examples/ directory. Each demonstrates a different feature or use case.

To run any example:

conda activate t3_env
cd ~/Code/T3/examples/<example_name>
python ~/Code/T3/T3.py input.yml

Minimal

Directory: examples/minimal/

The simplest complete T3 input: H2/O2 combustion with Cantera-based sensitivity analysis and ARC for QM refinement. A good starting point for new users.

Features demonstrated:

  • Basic species definition with SMILES and concentrations
  • CanteraConstantTP adapter for sensitivity analysis
  • SA_observable on H and OH
  • ARC QM with a simple level of theory (b3lyp/6-31g(d,p))
  • Progressive core_tolerance: [0.01, 0.001]

Cantera SA

Directory: examples/cantera_sa/

Demonstrates using a Cantera simulation adapter for sensitivity analysis with global observables.

Features demonstrated:

  • CanteraConstantTP adapter
  • global_observables: ['IDT'] for ignition delay time sensitivity
  • Three-stage core_tolerance: [0.01, 0.005, 0.001]
  • Species-level SA observables (OH, H)

Shock tube

Directory: examples/shock_tube/

Idealized reflected-shock experiment for H2/O2/Ar. A shock tube post-shock state is treated as a closed, adiabatic, constant-volume batch reactor.

Features demonstrated:

  • CanteraConstantUV adapter — closed adiabatic constant-V batch
  • Dilute mixture in argon (balance: true on Ar, reactive: false)
  • global_observables: ['IDT'] — IDT is the primary measurement of a shock tube
  • Short termination_time in milliseconds, matching typical IDT magnitudes
  • Post-shock T = 1400 K, P = 2 bar

Plug flow reactor (PFR)

Directory: examples/pfr/

An isothermal, isobaric flow reactor (a Lagrangian parcel of gas advected at constant T and P) using the CanteraPFR adapter.

Features demonstrated:

  • CanteraPFR adapter — Lagrangian PFR
  • Residence time set via the reactor termination_time
  • Reactor geometry (LENGTH, AREA, N_CELLS) controlled by module-level constants in t3/simulate/cantera_pfr.py
  • Species-level SA observables (OH, H)

PFR with prescribed T(z) profile

Directory: examples/pfr_t_profile/

A non-isothermal, isobaric flow reactor in which the gas temperature follows a hard-coded axial profile T(z). Useful for flow-tube experiments where the wall temperature is known a priori (e.g., a measured profile). A single Lagrangian particle is advected through N_CELLS segments and the gas temperature at each segment is overridden from the profile (energy equation off); the velocity (and therefore the time step per segment) is recomputed from the local density at each T.

Features demonstrated:

  • CanteraPFRTProfile adapter — Lagrangian non-isothermal PFR
  • Default profile: 80 cm reactor, raised-cosine ramp 300 → 900 K over 20 cm, isothermal plateau at 900 K for 40 cm, raised-cosine ramp 900 → 500 K over 20 cm — C¹ continuous everywhere
  • Reactor geometry, breakpoints, and the temperature_profile(z) function are all controlled by module-level constants in t3/simulate/cantera_pfr_t_profile.py — advanced users either tune the constants in place or copy the file as the basis for a brand-new adapter
  • Mass flow is constant (set from the inlet density and the termination_time); density and velocity evolve with T
  • Sensitivity analysis is supported and indexed by axial position z (the reactor is steady-state in the lab frame). get_sa_coefficients() adds a 'distance' key to the standard sa_dict carrying the cell-center positions [m]

Jet stirred reactor (JSR)

Directory: examples/jsr/

An isothermal, isobaric, well-mixed steady-state reactor with continuous feed and outflow, using the CanteraJSR adapter.

Features demonstrated:

  • CanteraJSR adapter — JSR / PSR / CSTR
  • Inlet mass flow rate set so mdot = m_reactor / tau, with tau taken from the reactor termination_time
  • Reactor volume controlled by the module-level VOLUME constant in t3/simulate/cantera_jsr.py (defaults to 100 cm³)
  • Dilute fuel in nitrogen (balance: true on N2)
  • Species-level SA observables (OH, H)

Full QM workflow

Directory: examples/with_qm/

Shows the core T3 iterative workflow: RMG model generation followed by QM refinement with ARC, repeated over multiple iterations.

Features demonstrated:

  • Complete RMG + ARC iterative cycle
  • adaptive_levels for selecting level of theory based on species size:
    • Small species (1-6 heavy atoms): high-level CCSD(T)-F12
    • Medium species (7-14): DLPNO-CCSD(T)
    • Large species (15+): DFT only
  • Four-stage core_tolerance for progressive model refinement
  • Species constraints to limit model size
  • Balance species (N2)

Ranged conditions

Directory: examples/ranged_conditions/

Demonstrates running sensitivity analysis across a grid of temperatures, pressures, and concentrations.

Features demonstrated:

  • Temperature range: T: [800, 1500] K
  • Pressure range: P: [1, 10] bar
  • Concentration ranges on fuel and oxidizer: concentration: [0.10, 0.67]
  • Grid density control: num_sa_per_temperature_range, num_sa_per_pressure_range
  • modify_concentration_ranges_together: true to vary species together
  • conditions_per_iteration: 12 for RMG

Pressure dependence

Directory: examples/pressure_dependence/

Shows how to enable pressure-dependent network generation in RMG.

Features demonstrated:

  • pdep block with method: MSC (modified strong collision)
  • Chebyshev interpolation over a T-P grid
  • pdep_SA_threshold for PES-level sensitivity analysis
  • ME_methods: ['CSE', 'MSC'] for master equation analysis
  • max_atoms: 16 controlling which species are included in PDep networks
  • Species constraints to keep the model tractable

Pre-QM (iteration 0)

Directory: examples/pre_qm_iteration_0/

Demonstrates computing thermodynamic properties for key species before the first RMG iteration.

Features demonstrated:

  • QM species block with radicals to compute upfront (n-propyl, i-propyl, propylperoxyl)
  • seed_all_rads: ['radical', 'alkoxyl', 'peroxyl'] on the fuel to auto-generate radical derivatives
  • Pre-computed thermo available to RMG from iteration 1 onward
  • CBS-QB3 composite method for iteration 0 species

Liquid phase

Directory: examples/liquid_phase/

Demonstrates a liquid-phase simulation with a solvent species.

Features demonstrated:

  • liquid batch constant T V reactor type
  • Temperature range for the reactor
  • solvent: true on the water species
  • reactive: false on N2 (non-reactive dissolved gas)
  • all_core_species: true to calculate thermo for every core species
  • Liquid-phase specific species constraints

Input reference

For a comprehensive reference showing every available input argument with inline documentation, see the input reference page.