Computer Physics Communications Program LibraryPrograms in Physics & Physical Chemistry |

[Licence| Download | New Version Template] aenw_v1_0.tar.gz(1362 Kbytes) | ||
---|---|---|

Manuscript Title: RPMDrate: bimolecular chemical reaction rates from ring polymer molecular dynamics | ||

Authors: Yu. V. Suleimanov, J. W. Allen, W. H. Green | ||

Program title: RPMDrate | ||

Catalogue identifier: AENW_v1_0Distribution format: tar.gz | ||

Journal reference: Comput. Phys. Commun. 184(2013)833 | ||

Programming language: Fortran 90/95, Python (version 2.6.x or later, including any version of Python 3, is recommended). | ||

Computer: Not computer specific. | ||

Operating system: Any for which Python, Fortran 90/95 compiler and
the required external routines are available. | ||

Has the code been vectorised or parallelized?: The program can efficiently utilise 4096+ processors, depending on problem and available computer. At low temperatures, 110 processors is reasonable for a typical umbrella integration run with an analytic potential energy function and gradients on the latest x86-64 machines. | ||

RAM: 256 Mb | ||

Keywords: Ring polymer molecular dynamics, Chemical reaction rates, Kinetics, Reaction coordinate, Quantum effects, Tunneling, Zero point energy. | ||

Classification: 16.12. | ||

External routines: - NumPy (http://numpy.scipy.org, version 1.5.0 or later is recommended).
- FFTW3 (http://www.fftw.org, version 3.3 or later is recommended).
| ||

Nature of problem:The RPMDrate program calculates thermal bimolecular rate coefficients of thermally activated atom-diatom and more complex bimolecular chemical reactions in the gas phase. | ||

Solution method:The RPMD rate is calculated using the Bennett-Chandler factorization as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (transmission coefficient) factor. A key feature of this procedure is that it does not require that one calculate the absolute quantum mechanical partition function of the reactants or the transition state. The centroid density QTST rate is calculated from the potential of mean force along the reaction coordinate using umbrella integration. The reaction coordinate is taken to be an interpolating function that connects two dividing surfaces: one located in the asymptotic reactant valley and the other located in the transition state region. The Hessian of the collective reaction coordinate is obtained analytically. The transmission coefficient is calculated from the RPMD simulations with the hard constraint along the reaction coordinate. | ||

Restrictions:The applicability of RPMDrate is restricted to global potential energy surfaces with gradients. In the current release, they should be provided by Python callable objects. | ||

Unusual features:Simple and user-friendly input system provided by Python syntax. | ||

Additional comments:Test calculations for the H + H _{2} reactions were
performed using the Boothroyd-Keogh-Martin-Peterson-2 (BKMP2)
potential energy surface (PES) [1]. PESs for the H + CH_{4}, OH + CH_{4} and H + C_{2}H_{6} reactions are taken from the online POTLIB library [2]. PESs are included within the distribution package as Fortran subroutines. Implementations of the colored-noise, generalized Langevin
equation (GLE) thermostats [3-5] have been included in the current release.The distribution contains example data and a detailed manual describing the use of RPMDrate. | ||

Running time:Highly dependent on the input parameters. The running time of RPMDrate depends mainly on the complexity of the potential energy surface and number of ring polymer beads. For the H + H _{2}, H
+ CH_{4}, and OH + CH_{4} test calculations given (with 128 ring polymer beads and analytic gradients), the running time is approximately 1800,
3600 and 4000 processor hours, respectively, on the Silicon Mechanics
nServ A413 servers. | ||

References: | ||

[1] | A.I. Boothroyd, W.J. Keogh, P.G. Martin, M.R. Peterson, J. Chem. Phys. 104 (1996) 7139. | |

[2] | R.J. Duchovic, Y.L. Volobuev, G.C. Lynch, A.W. Jasper, D.G. Truhlar, T.C. Allison, A.F. Wagner, B.C. Garrett, J. Espinosa-García J. C. Corchado, POTLIB, http://comp.chem.umn.edu/potlib. | |

[3] | M. Ceriotti, G. Bussi, M. Parrinello, J. Chem. Theory Comput. 6 (2010) 1170. | |

[4] | M. Ceriotti, G. Bussi, M. Parrinello, Phys. Rev. Lett. 103 (2009) 030603. | |

[5] | M. Ceriotti, G. Bussi, M. Parrinello, Phys. Rev. Lett. 102 (2009) 020601. |

Disclaimer | ScienceDirect | CPC Journal | CPC | QUB |