Create Input File

This form will generate an input file for a RMG-Py job. For more detailed explanations of each option, please see the documentation.


If you already have a saved input.py file that you would like to modify, you can upload it here to load it into the form for easy editing and saving.


  1. Thermodynamics Libraries

    Select the thermochemistry libraries you would like to be included in your RMG job in order of priority. You may select multiple libraries. If no libraries are selected, RMG will estimate all species' thermochemistry through Benson group additivity. We recommend using at least the 'primaryThermoLibrary'.

    You can browse the available libraries here: Thermodynamics Libraries

    Library
  2. Reaction Libraries and Seed Mechanisms

    Select reaction libraries you would like to be included in your RMG job in order of priority. Rates from reactions within the library will be used if the reaction is found in your job. You may select multiple libraries. If no libraries are selected, RMG will estimate kinetic rates using RMG-database rate rules alone.

    Normally, the kinetic library of reactions is used to estimate a reaction found on the edge. However, if you believe the reactions should be included within the mechanism core, select the "SeedMech" option to force the entire library to be added to the core. If you do not wish for these reactions to be automatically included in the core but do want to retain it in your mechanism, you may select the "Edge" option instead.

    You can browse the available libraries here: Kinetics Libraries

    Library SeedMech Edge
  3. Reactor Species:

    Use this form to add a species to the RMG job using its adjacency list. The "name" field will be used throughout your mechanism to identify this species. You can quickly fill in the adjacency list part of the form by entering any species identifier, such as a SMILES, InChI, CAS number, or species name in the "species identifier" field and pressing tab. This is translated into an adjacency list using the NCI Chemical Identifier Resolver.

  • Species Name:
    Species Identifier:
    Adjacency List:
    Mole Fraction:
    Inert Species:
  1. Reactor Systems

    Enter individual reactor system settings for which the RMG model will be valid. You may add multiple reactor systems for which the overall mechanism will be valid.

    You must provide a maximum reaction time for the job. A species conversion requirement is optional - be sure to use the same species name as provided previously. The RMG job will stop as soon as one of the termination criteria is fulfilled.

    RMG is also able to perform sensitivity analysis, provided it was compiled with the DASPK solver. To enable sensitivity analysis, provide the species that the analysis should be done for. Multiple species should be comma separated. The sensitivity threshold is the minimum sensitivity to be saved to the output file.

  • Temperature:
    Pressure:

    Termination Criteria:

    End Time:
    Species: Conversion:

    Sensitivity Analysis:

    Species:
    Threshold:
  1. Tolerances

    Indicate your allowed flux tolerance for moving a reaction from the edge to the core. In advanced options, you can set additional tolerances for the solver, and for the edge reactions (the possible reactions generated from the species in the core). Generally, the edge tolerance is set to zero unless you need to prune the edge to reduce model generation time and memory consumption. For more information on filtering reactions, click here. For more information on pruning, please see the documentation.

    Core Tolerance:
  • Advanced Options
    1. Filter Reactions:

      Pruning parameters

      Edge Tolerance:
      Tolerance to Interrupt Simulation:
      Maximum Number of Allowed Edge Species:
      Minimum Number of Core Species Before Pruning:
      Number of Iterations a Species Must Exist Before Pruning:

      Numerical Solver

      Absolute Tolerance:
      Relative Tolerance:
      Sensitivity Absolute Tolerance:
      Sensitivity Relative Tolerance:


  1. Pressure Dependence:

    If you would like to generate a pressure-dependent model, please select the pressure dependence method (above) as well as the interpolation model (Chebyshev or Pdep Arrhenius) you would like RMG to use. See advanced options to set the number of interpolation points, grain size, or number of basis function for Chebyshev interpolation.

    Model:
    Temperature Range: to
    Pressure Range: to
  • Advanced Options
    1. Maximum Atoms of Isomers in Network

      Maximum Atoms:
      If used, the number of maximum atoms turns off pressure dependence for molecules with atoms greater than the number specified. This is due to faster internal rate of energy transfer for larger molecules.

      Number of Interpolation Points Used in Model

      Temperature:
      Pressure:

      Grain Size

      Maximum Size:
      Minimum Number:

      Number of Basis Functions Used in Model (For Chebyshev Only)

      Temperature:
      Pressure:


  1. Quantum Calculations

    Optional block for performing on the fly quantum mechanical calculations to determine thermodynamic parameters. Calculations are only performed for molecules not present in the specified thermo libraries.

    Software:
    Method:
    Only Cyclics:
    It is recommended that Only Cyclics is set to True, since it is very time consuming to perform QM jobs on non-cyclic molecules, and it is likely that group additivity values will be more accurate.
    Maximum Radical Number:
    It is recommended that Maximum Radical Number be set to 0, because semi-empirical methods such as PM3, PM6, and PM7 are generally fitted with nonradical species, and therefore quantum calculations on radical species may not be accurate. Thermochemistry for radicals is computed by applying a Hydrogen Bond Increment value onto the neutral species to produce the most accurate value.
  • Advanced Options
    1. You may provide user specified directories for where to store thermo files as well as the the temporary scratch files. The default directories are QMfiles and QMscratch, respectively, in your job directory.
      File Store:
      Scratch Directory:


  1. Generated Species Constraints

    Optional constraints on allowed species. Species exceeding these constrainted will not be included in the model. In advanced options, allowing input species, seed mechanisms, or reaction libraries lets them bypass these constraints. For more information regarding singlet O2, please see Representing Oxygen.

    Maximum Carbon Atoms:
    Maximum Oxygen Atoms:
    Maximum Nitrogen Atoms:
    Maximum Silicon Atoms:
    Maximum Sulfur Atoms:
    Maximum Heavy Atoms (Non-Hydrogen):
    Maximum Radical Electrons:
  • Advanced Options
    1. Allow Input Species:
      Allow Seed Mechanisms:
      Allow Reaction Libraries:
      Allow Singlet O2:


  1. Additional Options

    Restart files can be generated automatically during the progress of a RMG-Py job in order to pick up a job in the middle of a run rather than starting completely from scratch if there is a failure or memory issue. The save restart period may be optionally left empty if no restart files are desired. Note that saving restart files for large models can take a significant amount of time, so use caution when selecting the restart period. Explanations for the other options can be found here.

    Save Restart:
    Generate Output HTML (Draw molecules and save model to HTML):
    Generate Performance Statistics Plots:
    Save Concentration Profiles:
    Save Edge Species:
    Verbose Chemkin Comments:


By pressing submit, you will be prompted to save an input.py file ready for use in RMG-Py.