Distributed Codes

Summary. A new master equation solver featuring the strategies detailed in Y. Georgievskii, J. A. Miller, M. P. Burke, and S. J. Klippenstein, Reformulation and Solution of the Master Equation for Multiple-Well Chemical Reactions, J. Phys. Chem. A, 117, 12146-12154 (2013).

Notable Features

• An arbitrary number of wells and bimolecular species may be treated without specifying a preferred reactant
• Rate constants for all channels are computed simultaneously at multiple temperatures and pressures
• The numerical grids are automatically generated

Manual. Updated March 23, 2016 [PDF] [DOC]

Code. MESS.2020.1.24 [TGZ]

Standard Libraries
MPACK;Multiple precision arithmetic BLAS (MBLAS) and LAPACK (MLAPACK) [TGZ]
SLATEC Common Mathematical Library [TGZ]

Auxiliary Codes
MESS_TPfit [TGZ] written by Franklin Goldsmith

Examples. [TGZ]

Contact. Stephen Klippenstein [[email protected]]

References

The preferred citation for this code is

Y. Georgievskii and S. J. Klippenstein, MESS.2016.3.23.

Y. Georgievskii, J. A. Miller, M. P. Burke, and S. J. Klippenstein, Reformulation and Solution of the Master Equation for Multiple-Well Chemical Reactions, J. Phys. Chem. A, 117, 12146-12154 (2013) [DOI]

Developers. Y. Georgievskii, C. F. Goldsmith, J. A. Miller, M. P. Burke, and S. J. Klippenstein

Summary. A code for performing variable reaction coordinate transition state theory calculations. The calculations may be performed through interfacing with a user supplied analytic potential energy surface or with direct ab initio evaluations through interfacing with the MOLPRO and GAUSSIAN electronic structure codes.

Notable Features

• Arbitrary numbers of pivot points for each fragment
• Facile sampling over pivot point locations and separations
• One-dimensional correction potentials applied through user supplied routines

Manual. Updated March 23, 2016 [PDF] [DOC]

Examples. Updated March 23, 2016 [TGZ]

Code. VaReCoF.2016.3.23 [TGZ]

Code. VaReCoF.2017.5.19 [TGZ]

Contact. Stephen Klippenstein [[email protected]]

References

The preferred citations for this code are

(1) Y. Georgievskii, L. B. Harding, and S. J. Klippenstein, VaReCoF 2016.3.23.

(2) L. B. Harding, Y. Georgievskii, S. J. Klippenstein, Predictive Theory for Hydrogen Atom - Hydrocarbon Radical Association Kinetics. J. Phys. Chem. A, 109, 4646-4656 (2005).

Y. Georgievskii, S. J. Klippenstein, Transition State Theory for Multichannel Addition Reactions: Multifaceted Dividing Surfaces. J. Phys. Chem. A, 107, 9776-9781 (2003).

Y. Georgievskii, S. J. Klippenstein, Variable Reaction Coordinate Transition State Theory: Analytic Results and Application to the C2H3+H → C2H4 Reaction. J. Chem. Phys. 118, 5442-5455 (2003).

S. J. Klippenstein, Variational Optimizations in the Rice-Ramsberger-Kassel-Marcus Theory Calculations for Unimolecular Dissociations with No Reverse Barrier. J. Chem. Phys. 96, 367-371 (1992).

Developers. Yuri Georgievskii, Lawrence B. Harding, and Stephen J. Klippenstein

Summary. DiNT is a classical trajectory program for computing adiabatic and nonadiabatic chemistry. The code has a variety of options for preparing initial conditions, for performing final state analyses, and for semiclassical nonadiabatic propagation. The user may supply their own analytic potential energy surface, use one of the previously developed surfaces included in the distribution, or perform direct dynamics calculations. Recent applications include collisional energy transfer and spin-forbidden kinetics calculations.

Manual. Version 1.1, July 4, 2013 [PDF]

Code. Version 1.1, July 4, 2013 [TGZ]

TB+exp/6. A potential energy surface subroutine with parameterizations for C_xH_y + M [Fortran 77]

Contact. Ahren Jasper [[email protected]]

References

The preferred citations for this code are

(1) A. W. Jasper, C. M. Oana, and D. G. Truhlar, DiNT, July 2013.
(2) A. W. Jasper and D. G. Truhlar, "Non-Born–Oppenheimer molecular dynamics for conical intersections, avoided crossings, and weak interactions," in Conical Intersections: Theory, Computation, and Experiment, edited by W. Domcke, D. R. Yarkony, and H. Koppel (World Scientific, 2011), pp. 375-412 (chp. 10) or Adv. Ser. Phys. Chem. 17, 375-412 (2011).

Summary. This code can be used to

• Refine the geometry of a good MSX guess (MSXs are often called MECPs)
• Compute Landau-Zener NST (often called NA TST) rates
• Generate the requisite data files for use in MESS and VariFlex

Manual. October 26, 2023 [TXT]

Code. October 26, 2023 [TGZ]

Contact. Ahren Jasper [[email protected]]

References

The MSX optimization strategy is from

M. J. Bearpark, M. A. Robb, and H. B. Schlegel, Chem. Phys. Lett. 223, 269 (1994)

J. N. Harvey and M. Aschi, Phys. Chem. Chem. Phys. 1, 5555 (1999)

J. N. Harvey, Phys. Chem. Chem. Phys. 9, 331 (2007)
A. W. Jasper, J. Phys. Chem. A 119, 7339 (2015)

Summary. Lennard-Jones parameters are calculated from full-dimensional intermolecular potentials via one-dimensional minimizations averaged over the colliding partners' relative orientations. This method includes the effect of local anisotropy in the interaction potential and was shown to lead to very accurate predictions of Lennard-Jones collision rates as compared with tabulated values and with higher-level classical diffusion coefficients.

Manual. October 26, 2023 [TXT]

Code. October 26, 2023 [TGZ]

Contact. Ahren Jasper [[email protected]]

References

The preferred citation for this code and for the one-dimensional minimization method is

(1) A. W. Jasper and J. A. Miller, "Lennard-Jones parameters for combustion and chemical kinetics modeling from full-dimensional intermolecular potentials," Combust. Flame, 161, 101 (2014). [DOI]
(2) A. W. Jasper and J. A. Miller, OneDMin, October 2023.

(3) A. W. Jasper, J. A. Miller, and S. J. Klippenstein, "First-principles binary diffusion coefficients for H, H2, and four normal alkanes + N2," J. Chem. Phys. 141, 124313 (2014). [DOI]

(4) A. W. Jasper and J. A. Miller, "Theoretical unimolecular kinetics for CH4 + M → CH3 + H + M in eight baths, M = He, Ne, Ar, Kr, H2, CO, N2, and CH4," J. Phys. Chem. A 115, 6438 (2011) [DOI]

and validated for larger systems in

(5) A. W. Jasper, C. M. Oana, and J. A. Miller, "'Third-body' collision efficiencies for combustion modeling: Hydrocarbons in atomic and diatomic baths," Proc. Combust. Inst. 34 197-204 (2015). [DOI]
(6) A. W. Jasper, "'Third-body' collision parameters for hydrocarbons, alcohols, and peroxides and an effective internal rotor approach for estimating them," Int. J. Chem. Kinet. 52, 387–402 (2020). [DOI]

Summary. AutoMech is an Open-Source Programming Package designed for large-scale, high-level computational thermochemistry and kinetics.

Code. AutoMech [AutoMech page]

Contact. Stephen Klippenstein [[email protected]]

References

The preferred citation for this code is

S. N. Elliott, K. B. Moore, A. V. Copan, M. Keceli, C. Cavallotti, Y. Georgievskii, S. F. Schaefer, and S. J. Klippenstein. Automated theoretical chemical kinetics: predicting the kinetics for the initial stages of pyrolysis. Proc. Combust. Inst., 38:375–384, 2021. doi:10.1016/j.proci.2020.06.019