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July 6, 2022

TUMME 3.0: Tsinghua University Minnesota Master Equation program

by

Rui Ming Zhang,a,b Xuefei Xu,a and Donald G. Truhlarb

aCenter for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China

bDepartment of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, USA


TUMME status:

Most recent version: 3.0
Date of most recent version: July 6, 2022
Date of most recent manual update: July 6, 2022
Notes:
     When the code is updated, the version number and date are changed.
     If only the manual is revised, only the manual date is changed.

Summary

     TUMME (Tsinghua University Minnesota Master Equation solver) is a computer program for setting up and solving one-dimensional energy-dependent master equations for chemical kinetics of unimolecular and bimolecular reactions. For mechanisms involving only unimolecular isomerization (no bimolecular pairs), TUMME solves a conservative master equation for both rate constants and time-dependent energy-bin populations. For mechanisms involving bimolecular pairs, TUMME solves two kinds of master equation: (i) a nonconservative master equation for calculating rate constants of bimolecular reactions and (ii) a conservative master equation that includes bimolecular association in the transition matrix for calculating the time-evolution of the concentration of a pseudo-first-order bimolecular reactant. TUMME has interfaces to Gaussian, Polyrate, and/or MSTor output files that allow the master equation code to provide the microcanonical flux coefficients needed for the kernel of the ME as calculated by multi-structural variational transition state theory with small-curvature tunneling (MS-VTST/SCT). TUMME is written in double precision with Python 3; quadruple and octuple precision is also available for some subtasks in C++. The Python code can run in serial or parallel (MP or MPI), and C++ code can run on a single processor or on multiple processors with OpenMP.

     TUMME can treat both unimolecular reactions and bimolecular reactions, but bimolecular reactions are treated only in the limit of pseudo-first-order kinetics. TUMME can treat two kinds of master equation, with the difference being the way that one treats the bimolecular pairs. One kind of master equation is conservative (also called reversible or homogeneous); this kind of master equation leads to equilibrium. The other kind of master equation is nonconservative (also called irreversible or inhomogeneous); for mechanisms involving unimolecular dissociation, this kind of master equation leads to all isomers vanishing because one includes the dissociation reactions but not the reverse association reactions. If there are no bimolecular species in the mechanism, the master equation is always conservative. For mechanisms involving bimolecular pairs, TUMME uses the nonconservative master equation to extract phenomenological rate constants and uses the conservative master equation to calculate the time evolution of concentrations and energy-bin populations.

Features of TUMME:

  • A program for assembling and solving master equations for gas-phase chemical kinetics
  • Based on chemically significant eigenmodes [Y. Georgievskii, J. A. Miller, M. P. Burke, S. J. Klippenstein, J. Phys. Chem. A 117 (2013) 12146]
  • Calculates microcanonical flux coefficients (input to master equation) by multi-structural variational transition state theory with small-curvature tunneling (MS-VTST/SCT) or by conventional transition state theory by using data read from output files of Gaussian, Polyrate, and/or MSTor
  • Written in double precision with Python 3
  • Quadruple and octuple precision are also available for some subtasks in C++
  • Python code can run in serial or parallel (MP or MPI), and C++ code can run on a single processor or on multiple processors with openMP

    User manual:

    TUMME 3.0 Manual in PDF format

    Licensing and downloading:

    TUMME 3.0 is licensed under the Apache License, Version 2.0.
    The manual of TUMME 3.0 is licensed under CC-BY-4.0.

    Publications of results obtained with the TUMME 3.0 software should cite the program and/or the article describing the program.

    No guarantee is made that this software is bug-free or suitable for specific applications, and no liability is accepted for any limitations in the mathematical methods and algorithms used within. No consulting or maintenance services are guaranteed or implied.

    The use of the TUMME 3.0 implies acceptance of the terms of the licenses. The software may be downloaded here.

    Citations:

    Publications of results obtained with the TUMME 3.0 software should cite the program and/or the article describing the program.

    Other reading:

    Users of TUMME may also find the following application papers to be of interest:

    Acknowledgment:

    The U.S. Department of Energy, Office of Basic Energy Sciences is gratefully acknowledged.

    Links to other pages of interest:


    This document last modified on Oct. 20, 2022
    Updated by:  Software Manager