input.yml

# A commented version of T3 input file
project: project_name  # required
project_directory: project_name  # optional

verbose: 20  # The logging level, optional. 10 - debug, 20 - info, 30 - warning, default: 20
             # ``None`` will avoid logging to file.

# arguments related to T3 (optional)
t3:

  # options (optional block, all arguments have defaults)
  options:
    flux_adapter: RMG  # optional, can use any implemented simulation adapter, default: 'RMG'
    profiles_adapter: RMG  # optional, can use any implemented simulation adapter, default: 'RMG'
    collision_violators_thermo: false  # optional, whether to calculate thermo of species participating in collision violating reactions, default: ``False``
    collision_violators_rates: false  # optional, whether to calculate rates of core collision violating reactions, default: ``False``. If ``True``, will only be done if all thermo of species in these reactions were calculated (will force ``collision_violators_thermo`` to be ``True`` if it's not
    all_core_species: false  # optional, whether to calculate thermo for all core species, default: ``False``
    all_core_reactions: false  # optional, whether to calculate rates (to be implemented) for all core species, default: ``False``
    fit_missing_GAV: false  # optional, whether to capture wrong thermo groups of species estimated by RMG and attempt to calculate them, default: ``False``
    max_T3_iterations: 10  # optional, maximum T3 iterations, default: 10
    max_RMG_exceptions_allowed: 10  # optional, maximum number of times RMG is allowed to crash, default: 10
    max_RMG_walltime: '00:02:00:00'  # optional, default: ``None``
    max_T3_walltime: '01:00:00:00'  # optional, default: ``None``
    library_name: T3  # optional, default: 'T3'
    save_libraries_directly_in_rmgdb: False  # optional, whether to save the RMG kinetics and thermo libraries directly in the RMG-database repository, default: ``False``
    num_sa_per_temperature_range: 3  # optional, if a range of temperatures is given this argument specifies how many equally distributed points to generate for local SA runs, default: 3
    num_sa_per_pressure_range: 3  # optional, if a range of pressures is given this argument specifies how many equally distributed points to generate for local SA runs, default: 3
    num_sa_per_volume_range: 3  # optional, if a range of volumes is given this argument specifies how many equally distributed points to generate for local SA runs, default: 3
    num_sa_per_concentration_range: 3  # optional, if a species concentration is given as a range this argument specifies how many equally distributed points to generate for local SA runs, default: 3
    modify_concentration_ranges_together: True  # optional, if species concentration is given as a range, whether to vary the concentration of different species together (``True``) or to create combination when running local SA (``False``) - warning setting this to ``False`` may result in many combinations, especially if num_sa_per_concentration_range is set to a high value, and will spawn many SA runs which could be very slow, default: ``True``
    modify_concentration_ranges_in_reverse: False  # optional, if species concentration is given as a range for two species only (e.g., fuel and oxidizer), whether to vary the concentration of the species inversely (in this case, you should define the concentration of N2 in an air mixture as ``balance: true``, default: ``False``

  # sensitivity analysis (optional block, T3 can run w/o SA)
  sensitivity:
    adapter: RMGConstantTP  # *required* (this is how SA is requested), can use any implemented simulation adapter
    atol: 1e-6  # optional, default: 1e-6
    rtol: 1e-4  # optional, default: 1e-4
    global_observables: ['IgD', 'ESR', 'SL']  # optional, only implemented in the Cantera adapter, default: ``None``
    SA_threshold: 0.01  # optional, default: 0.01
    pdep_SA_threshold: 0.001  # optional, used to determine wells and reactions (to be implemented) to calculate
                              # thermo and rates for from a PES of a sensitive reaction, default: 0.001
                              # Pass ``None`` to skip PES SA.
    ME_methods: ['CSE', 'MSC']  # master equation methods, used to conduct a PES SA,
                                # could be any combination of 'CSE', 'RS', 'MSC', default: ['CSE', 'MSC']
    top_SA_species: 10  # optional, used per observable to determine thermo to calculate, default: 10
    top_SA_reactions: 10  # optional, used per observable to determine rates to calculate (to be implemented) as well as
                          # thermo of species participating in these reactions, default: 10

  # uncertainty analysis for a predicted species concentration (optional block, T3 can ran w/o UA)
  # either local or global UA type must be specified to execute an UA
  uncertainty:
    adapter: RMG  # *required* (this is how UA is requested), currently only implemented in the RMG adapter
    local_analysis: false  # optional, local uncertainty analysis using first-order sensitivity coefficients, default: ``False``
    global_analysis: false  # optional, global uncertainty analysis varying largest sensitive input parameters, default: ``False``
    correlated: true  # optional, whether to treat input parameters as correlated (RMG has ``correlated`` and ``uncorrelated``, ascribe correctly), default: ``True``
    local_number: 10  # optional, the number of reported parameters in a local uncertainty analysis, default: 10
    global_number: 5  # optional, number of sensitive input parameters to vary in the global uncertainty analysis per observable, applies independently to species and reactions, default: 5
    termination_time: None  # only necessary for global UA if a termination time wasn't specified in the RMG reactor
    PCE_run_time: 1800  # optional, sets a time limit for adapting the Polynomial Chaos Expansion (PCE) to the output, default: 1000, Units: s
    PCE_error_tolerance: None  # optional, sets the target L2 error between the PCE model and the true output, default: ``None``
    PCE_max_evals: None  # optional, sets a limit on the total number of model evaluations used to adapt the PCE, default: ``None``
    logx: false  # optional, toggles the output parameter space between mole fractions and log mole fractions, results in mole fraction space are more physically meaningful, while results in log mole fraction space can be directly compared against local uncertainty results, default: ``False``

# arguments related to RMG, required
rmg:

  # general
  rmg_execution_type: incore  # optional, determines how to execute RMG. Currently, `incore` (running in the same process) and `local` (submitting to the local server queue, not via SSH) are supported. This argument is set from T3's settings.py file unless explicitly given here, default: ``None``
  memory: 15  # optional, specifies the RMG memory to be used when executing on a server, units are GB. This argument is set from T3's settings.py file unless explicitly given here, default: ``None``

  # database (a required block)
  database:
    thermo_libraries: ['BurkeH2O2', 'DFT_QCI_thermo', 'primaryThermoLibrary', 'CBS_QB3_1dHR']  # *required*, can be an empty list
    kinetics_libraries: ['BurkeH2O2inN2', 'NOx2018', 'Klippenstein_Glarborg2016']  # *required*, can be an empty list
    transport_libraries: ['PrimaryTransportLibrary', 'OneDMinN2', 'NOx2018', 'GRI-Mech']  # optional, default: ['PrimaryTransportLibrary', 'OneDMinN2', 'NOx2018', 'GRI-Mech']
    seed_mechanisms: []  # optional, default: []
    kinetics_depositories: default  # optional, default: 'default'
    kinetics_families: default  # optional, default: 'default'
    kinetics_estimator: rate rules  # optional, default: 'rate rules'

  # species (initial mixture) (a required block)
  # concentration units are mole fraction for gas phase and mol/cm3 for liquid phase
  # must specify either `smiles`, 'inchi', or `adj`
  # not specifying `concentration` is allowed and will result in a 0 initial concentration.
  species:
    - label: ethane
      smiles: CC
      concentration: [1, 1.75]  # a concentration range can be defined (a length-2 list)
      reactive: true  # optional, default: ``True``
      xyz: [ethane.log]  # each entry could be a string/dictionary XYZ format or a file path to parse the information from
      seed_all_rads: ['radical', 'alkoxyl', 'peroxyl']  # radical derivatives that will be added the RMG input file
    - label: OH
      smiles: '[OH]'
      observable: true  # optional, will be used as both SA and UA observable, default: ``False``
      SA_observable: true  # optional, will be used as an SA observable, default: ``False``
      UA_observable: true  # optional, will be used as an UA observable, default: ``False``
    - label: O2
      smiles: '[O][O]'
      concentration: 3.5
    - label: N2
      adjlist: |
        1 N u0 p1 c0 {2,T}
        2 N u0 p1 c0 {1,T}
      concentration: 3.5 * 3.76
      constant: true  # optional, only allowed to be ``True`` in liquid phase simulations, default: ``False``
      balance: true  # optional, only allowed to be ``True`` in gas phase simulations, default: ``False``
    - label: water
      smiles: O
      solvent: true  # optional, only allowed to be ``True`` in liquid phase simulations, required for one species for liquid phase simulations, default: ``False``

  # reactors (List[dict]) (a required block)
  # reactor type can be either 'gas batch constant T P', or 'liquid batch constant T V'
  # at least one of the three termination criteria must be given per reactor
  # note that having a termination time is recommended, it will also be used for the simulations
  # for species concentration profiles and SA. If not specified, the chemical time at which RMG terminated due to other
  # termination criteria will be used.
  # users may specify as many reactors as they wish, yet the must all be either gas or liquid phase
  reactors:
    - type: gas batch constant T P
      T: [800, 1750]  # Could be a float (single T) or a list (range of Ts), Units: K
      P: 1e0  # could be a float (single P) or a list (range of P), Units: bar
      termination_conversion:
        'ethane': 0.2
      termination_time: [5, 's']  # allowed units: 'micro-s', 'ms', 's', 'hours', 'days'
      termination_rate_ratio: 0.01
      conditions_per_iteration: 12  # optional, number of times variable ranged-reactor conditions are ran per RMG iteration (nSims)

  # model (a required block)
  model:
    # primary_tolerances:
    core_tolerance: [0.05, 0.01]  # *required*, float or list (if a list, a different core tolerance value is used per T3 iteration) (toleranceMoveToCore)
    atol: 1e-16  # optional, default: 1e-16
    rtol: 1e-8  # optional, default: 1e-8
    # filtering:
    filter_reactions: false  # optional, filtering reactions
    filter_threshold: 1e+8  # optional, filtering reactions
    # pruning:
    tolerance_interrupt_simulation: [0.05, 0.01]  # optional, float or list, pruning, will be set equal to core_tolerance if not specified
    min_core_size_for_prune: 50  # optional, pruning
    min_species_exist_iterations_for_prune: 2  # optional, pruning
    tolerance_keep_in_edge: 0.02  # optional, pruning
    maximum_edge_species: 1000000  # optional, pruning
    tolerance_thermo_keep_species_in_edge:  # optional, thermo pruning
    # staging:
    max_num_species: None  # optional, staging
    # dynamics:
    tolerance_move_edge_reaction_to_core:  # optional, dynamics criterion
    tolerance_move_edge_reaction_to_core_interrupt: 5.0  # optional, dynamics criterion
    dynamics_time_scale: (0.0, 'sec')  # optional, dynamics criterion
    # multiple_objects:
    max_num_objs_per_iter: 1  # optional, multiple objects
    terminate_at_max_objects: false  # optional, multiple objects
    # misc:
    ignore_overall_flux_criterion: false  # optional
    tolerance_branch_reaction_to_core: 0.001  # optional
    branching_index: 0.5  # optional
    branching_ratio_max: 1.0  # optional
    # surface algorithm
    tolerance_move_edge_reaction_to_surface: None
    tolerance_move_surface_species_to_core: None
    tolerance_move_surface_reaction_to_core: None
    tolerance_move_edge_reaction_to_surface_interrupt: None

  # pressure dependence (optional block)
  # only allowed for gas phase simulations
  pdep:
    method: MSC  # *required*, this is how PDep is requested
    max_grain_size: 2  # optional, units: kJ/mol, default: 2
    max_number_of_grains: 250  # optional, default: 250
    T: [300, 2500, 10]  # optional, [T min, T max, number of points], default: [300, 2500, 10], Units: K
    P: [0.01, 100, 10]  # optional, [P min, P max, number of points], default: [0.01, 100, 10], Units: bar
    interpolation: Chebyshev  # optional, either 'PDepArrhenius' or 'Chebyshev', default: 'Chebyshev'
    T_basis_set: 6  # optional, only used for a Chebyshev interpolation, default: 6
    P_basis_set: 4  # optional, only used for a Chebyshev interpolation, default: 4
    max_atoms: 16  # optional, default: 16

  # options (optional block)
  options:
    seed_name: Seed  # optional, name for the generated seed, default: 'Seed'
    save_edge: true  # optional, saves the Edge, default: ``True`` in T3 (``False`` in RMG) (saveEdgeSpecies)
    save_html: false  # optional, default: ``False`` (have T3 generate HTML for the core after the last T3 iteration))
    generate_seed_each_iteration: true  # optional, save a seed at each iteration, default: ``True``
    save_seed_to_database: false  # optional, save the seed to the database as well, default: ``False``
    units: si  # optional, currently RMG does not support any other units set
    generate_plots: false  # optional, will generate RMG job statistics plots (core and edge size, memory used), default: ``False``
    save_simulation_profiles: false  # optional, save RMG .csv simulation profiles files, default: ``False``
    verbose_comments: false  # optional, adds significant verbosity to the chemkin files, default: ``False``
    keep_irreversible: false  # optional, don't force library reactions to be reversible, default: ``False``
    trimolecular_product_reversible: true  # optional, allow families with three products to react in the reverse direction, default: ``True``
    save_seed_modulus: -1  # optional, save the seed every n iterations (-1 to only save the last iteration), default: -1

  # species constraints (optional block)
  species_constraints:
    allowed: ['input species', 'seed mechanisms', 'reaction libraries']  # optional, allow species from these sources to bypass the constraints, default: ['input species', 'seed mechanisms', 'reaction libraries']
    max_C_atoms: 10  # required
    max_O_atoms: 10  # required
    max_N_atoms: 10  # required
    max_Si_atoms: 10  # required
    max_S_atoms: 10  # required
    max_heavy_atoms: 10  # required
    max_radical_electrons: 2  # required
    max_singlet_carbenes: 1  # optional, default: 1
    max_carbene_radicals: 0  # optional, default: 0
    allow_singlet_O2: true  # optional, allows singlet O2 **from the input file**, default: ``True`` in T3 (``False`` in RMG)

# arguments related to QM calcs, required to run QM calcs, otherwise T3 will only spawn RMG
qm:
  # currently only ARC is supported, we'd like to also incorporate AutoTST
  # All legal ARC arguments are allowed here
  # Note: If ``species`` or ``reactions`` are specified, ARC will be spawned prior to RMG to calculate them first
  adapter: ARC
  # any legal ARC argument can come here
  adaptive_levels:
    (1, 6):
      opt_level: wb97xd/wb97xd/def2tzvp
      sp: ccsd(t)-f12/aug-cc-pvtz-f12
    (7, 30):
      conformer_level:
        method: wb97xd
        basis: def2svp
      opt_level:
        method: wb97xd
        basis: def2tzvp
      sp_level:
        method: dlpno-ccsd(T)
        basis: def2-tzvp
        auxiliary_basis: def2-tzvp/c
    (31, 'inf'):
      opt_level: wb97xd/wb97xd/def2tzvp
  species:
    - label: vinoxy
      smiles: C=C[O]