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A Modern-Fortran Program for Chemical Kinetics on Top of Anharmonic Vibrational Calculations

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Computational Science and Its Applications – ICCSA 2019 (ICCSA 2019)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 11624))

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Abstract

We discuss the design and implementation of StarRate, a modern-Fortran program for the calculation of chemical kinetics coupled to anharmonic vibrational perturbative treatments. The program is written in the F language, a carefully crafted subset of Fortran 95, and is conceived in an object-based programming paradigm, i.e. the set of object-oriented programming features supported by Fortran 90/95. StarRate is made up of three main modules handling the involved molecular species, the elementary reaction steps, and the whole reaction scheme. Input data are accessed through an XML interface based on a cross-code hierarchical data format granting interoperability with popular electronic-structure packages and with the graphical interface of the Virtual Multifrequency Spectrometer developed in our group. Data parsing is performed through versatile Python scripts. Test calculations on the isomerization reaction of C-cyanomethanimine using anharmonic densities of states obtained with a development version of Gaussian are reported together with an account of ongoing developments.

The research leading to these results has received funding from Scuola Normale Superiore through project “DIVE: Development of Immersive approaches for the analysis of chemical bonding through Virtual-reality Environments” (SNS18_B_RAMPINO) and program “Finanziamento a supporto della ricerca di base” (SNS_RB_RAMPINO). The authors are grateful to Dr. Daniele Licari (Scuola Normale Superiore) for fruitful discussions.

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Notes

  1. 1.

    Cardelli and Wegner identify using user-defined types for identity and classification without inheritance as object-based programming [6].

  2. 2.

    The partition function Q(T) can as well be computed from the density of states \(\rho (E)\) by a Laplace transform:

    figure a

    with \(k_\mathrm {B}\) being the Boltzmann constant and T being the absolute temperature.

References

  1. Ram, S.: Dr. Alan Kay on the meaning of Object-Oriented Programming (2003). http://www.purl.org/stefan_ram/pub/doc_kay_oop_en. Accessed 14 Mar 2019

  2. Frisch, M.J., et al.: Gaussian 16 Revision B.01. Gaussian Inc., Wallingford CT (2016)

    Google Scholar 

  3. Cary, J.R., Shasharina, S.G., Cummings, J.C., Reynders, J.V., Hinker, P.J.: Comparison of C++ and Fortran 90 for object-oriented scientific programming. Comput. Phys. Commun. 105(1), 20–36 (1997)

    MATH  Google Scholar 

  4. Decyk, V.K., Norton, C.D., Szymanski, B.K.: How to support inheritance and run-time polymorphism in Fortran 90. Comput. Phys. Commun. 115(1), 9–17 (1998)

    Google Scholar 

  5. Gorelik, A.M.: Object-oriented programming in modern Fortran. Program. Comput. Softw. 30(3), 173–179 (2004)

    MathSciNet  MATH  Google Scholar 

  6. Cardelli, L., Wegner, P.: On understanding types, data abstraction and polymorphism. ACM Comput. Surv. 17(4), 471–522 (1985)

    Google Scholar 

  7. Gray, M.G., Roberts, R.M., Dubois, P.F.: Object-based programming in Fortran 90. Comput. Phys. 11(4), 355–361 (1997)

    Google Scholar 

  8. Kim, Y.H., Lee, I.H., Martin, R.M.: Object-oriented construction of a multigrid electronic-structure code with Fortran 90. Comput. Phys. Commun. 131(1–2), 10–25 (2000)

    MATH  Google Scholar 

  9. Jayatilaka, D., Grimwood, D.J.: Tonto: a Fortran based object-oriented system for quantum chemistry and crystallography. In: Sloot, P.M.A., Abramson, D., Bogdanov, A.V., Gorbachev, Y.E., Dongarra, J.J., Zomaya, A.Y. (eds.) ICCS 2003. LNCS, vol. 2660, pp. 142–151. Springer, Heidelberg (2003). https://doi.org/10.1007/3-540-44864-0_15

    Chapter  Google Scholar 

  10. Zaghi, S.: OFF, open source finite volume fluid dynamics code: a free, high-order solver based on parallel, modular, object-oriented Fortran API. Comput. Phys. Commun. 185(7), 2151–2194 (2014)

    Google Scholar 

  11. Metcalf, M., Reid, J.: The F Programming Language. Oxford University Press Inc., New York (1996)

    MATH  Google Scholar 

  12. F Syntax Rules. http://www.fortran.com/F/F_bnf.html. Accessed 14 Mar 2019

  13. Rossi, E., et al.: Code interoperability and standard data formats in quantum chemistry and quantum dynamics: the Q5/D5Cost data model. J. Comput. Chem. 35(8), 611–621 (2014)

    Google Scholar 

  14. Rampino, S., Monari, A., Rossi, E., Evangelisti, S., Laganà, A.: A priori modeling of chemical reactions on computational grid platforms: workflows and data models. Chem. Phys. 398, 192–198 (2012)

    Google Scholar 

  15. Licari, D., Baiardi, A., Biczysko, M., Egidi, F., Latouche, C., Barone, V.: Implementation of a graphical user interface for the Virtual Multifrequency Spectrometer: the VMS-draw tool. J. Comput. Chem. 36(5), 321–334 (2015)

    Google Scholar 

  16. FoX in Fortran Wiki. http://fortranwiki.org/fortran/show/FoX. Accessed 14 Mar 2019

  17. Zaleski, D.P., et al.: Detection of E-cyanomethanimine toward Sagittarius B2(N) in the Green Bank Telescope PRIMOS survey. Astrophys. J. 765(1), L10 (2013)

    Google Scholar 

  18. Melosso, M., et al.: Laboratory measurements and astronomical search for cyanomethanimine. Astron. Astrophys. 609, A121 (2018)

    Google Scholar 

  19. Nandi, S., Bhattacharyya, D., Anoop, A.: Prebiotic chemistry of HCN tetramerization by automated reaction search. Chem. Eur. J. 24(19), 4885–4894 (2018)

    Google Scholar 

  20. Balucani, N.: Elementary reactions and their role in gas-phase prebiotic chemistry. Int. J. Mol. Sci. 10(5), 2304–2335 (2009)

    Google Scholar 

  21. Chakrabarti, S., Chakrabarti, S.K.: Can DNA bases be produced during molecular cloud collapse? Astron. Astrophys. 354, L6–L8 (2000)

    Google Scholar 

  22. Puzzarini, C.: Isomerism of cyanomethanimine: accurate structural, energetic, and spectroscopic characterization. J. Phys. Chem. A 119(47), 11614–11622 (2015)

    Google Scholar 

  23. Vazart, F., Calderini, D., Skouteris, D., Latouche, C., Barone, V.: Reassessment of the thermodynamic, kinetic, and spectroscopic features of cyanomethanimine derivatives: a full anharmonic perturbative treatment. J. Chem. Theor. Comput. 11(3), 1165–1171 (2015)

    Google Scholar 

  24. Rampino, S., Faginas Lago, N., Laganà, A., Huarte-Larrañaga, F.: An extension of the grid empowered molecular simulator to quantum reactive scattering. J. Comput. Chem. 33(6), 708–714 (2012)

    Google Scholar 

  25. Rampino, S., Skouteris, D., Laganà, A.: Microscopic branching processes: the O + O\(_2\) reaction and its relaxed potential representations. Int. J. Quantum Chem. 110(2), 358–367 (2010)

    Google Scholar 

  26. Rampino, S., Skouteris, D., Laganà, A.: The O + O\(_2\) reaction: quantum detailed probabilities and thermal rate coefficients. Theor. Chem. Acc. 123(3/4), 249–256 (2009)

    Google Scholar 

  27. Laganà, A., Faginas Lago, N., Rampino, S., Huarte Larrañaga, F., García, E.: Thermal rate coefficients in collinear versus bent transition state reactions: the N + N\(_2\) case study. Physica Scripta 78(5), 058116 (2008)

    MATH  Google Scholar 

  28. Rampino, S., Pastore, M., Garcia, E., Pacifici, L., Laganà, A.: On the temperature dependence of the rate coefficient of formation of C\(_2^+\) from C + CH\(^+\). Monthly Not. Roy. Astron. Soc. 460(3), 2368–2375 (2016)

    Google Scholar 

  29. Pacifici, L., Pastore, M., Garcia, E., Laganà, A., Rampino, S.: A dynamics investigation of the C + CH\(^+\)\(\rightarrow \) C\(_2^+\) + H reaction on an ab initio bond-order like potential. J. Phys. Chem. A 120(27), 5125–5135 (2016)

    Google Scholar 

  30. Rampino, S., Suleimanov, Y.V.: Thermal rate coefficients for the astrochemical process C + CH\(^+\)\(\rightarrow \) C\(2^+\) + H by ring polymer molecular dynamics. J. Phys. Chem. A 120(50), 9887–9893 (2016)

    Google Scholar 

  31. Rice, O.K., Ramsperger, H.C.: Theories of unimolecular gas reactions at low pressures. J. Am. Chem. Soc. 49(7), 1617–1629 (1927)

    Google Scholar 

  32. Kassel, L.S.: Studies in homogeneous gas reactions. I. J. Phys. Chem. 32(2), 225–242 (1927)

    Google Scholar 

  33. Marcus, R.A.: Unimolecular dissociations and free radical recombination reactions. J. Chem. Phys. 20(3), 359–364 (1952)

    Google Scholar 

  34. Brouard, M.: Reaction Dynamics. Oxford Chemistry Primers. OUP Oxford (1998)

    Google Scholar 

  35. Green, N.J.B.: Chapter 1 - introduction. In: Green, N.J., (ed.) Unimolecular Kinetics. Volume 39 of Comprehensive Chemical Kinetics, pp. 1–53. Elsevier (2003)

    Google Scholar 

  36. Barone, V.: Anharmonic vibrational properties by a fully automated second-order perturbative approach. J. Chem. Phys. 122(1), 014108 (2005)

    Google Scholar 

  37. Bloino, J., Biczysko, M., Barone, V.: General perturbative approach for spectroscopy, thermodynamics, and kinetics: methodological background and benchmark studies. J. Chem. Theor. Comput. 8(3), 1015–1036 (2012)

    Google Scholar 

  38. Stein, S.E., Rabinovitch, B.S.: Accurate evaluation of internal energy level sums and densities including anharmonic oscillators and hindered rotors. J. Chem. Phys. 58(6), 2438–2445 (1973)

    Google Scholar 

  39. Beyer, T., Swinehart, D.F.: Algorithm 448: number of multiply-restricted partitions. Commun. ACM 16(6), 379 (1973)

    Google Scholar 

  40. Wang, F., Landau, D.P.: Efficient, multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett. 86(10), 2050–2053 (2001)

    Google Scholar 

  41. Zhou, C., Bhatt, R.N.: Understanding and improving the Wang-Landau algorithm. Phys. Rev. E 72(2), 025701 (2005)

    Google Scholar 

  42. Basire, M., Parneix, P., Calvo, F.: Quantum anharmonic densities of states using the Wang-Landau method. J. Chem. Phys. 129(8), 081101 (2008)

    Google Scholar 

  43. Nguyen, T.L., Barker, J.R.: Sums and densities of fully coupled anharmonic vibrational states: a comparison of three practical methods. J. Phys. Chem. A 114(10), 3718–3730 (2010)

    Google Scholar 

  44. Frisch, M.J., et al.: Gaussian development version, revision i.13. Gaussian Inc., Wallingford CT (2018)

    Google Scholar 

  45. Lee, C., Yang, W., Parr, R.G.: Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785–789 (1988)

    Google Scholar 

  46. Becke, A.D.: Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98(7), 5648–5652 (1993)

    Google Scholar 

  47. Grimme, S., Ehrlich, S., Goerigk, L.: Effect of the damping function in dispersion corrected density functional theory. J. Comput. Chem. 32(7), 1456–1465 (2011)

    Google Scholar 

  48. Double and triple-\(\zeta \) basis sets of SNS families are available for download. http://smart.sns.it. Accessed 14 Mar 2019

  49. Bloino, J., Barone, V.: A second-order perturbation theory route to vibrational averages and transition properties of molecules: general formulation and application to infrared and vibrational circular dichroism spectroscopies. J. Chem. Phys. 136(12), 124108 (2012)

    Google Scholar 

  50. Rampino, S.: Configuration-space sampling in potential energy surface fitting: a space-reduced bond-order grid approach. J. Phys. Chem. A 120(27), 4683–4692 (2016)

    Google Scholar 

  51. Salvadori, A., Fusè, M., Mancini, G., Rampino, S., Barone, V.: Diving into chemical bonding: an immersive analysis of the electron charge rearrangement through virtual reality. J. Comput. Chem. 39(31), 2607–2617 (2018)

    Google Scholar 

  52. Bistoni, G., Rampino, S., Tarantelli, F., Belpassi, L.: Charge-displacement analysis via natural orbitals for chemical valence: charge transfer effects in coordination chemistry. J. Chem. Phys. 142(8), 084112 (2015)

    Google Scholar 

  53. Fusè, M., Rimoldi, I., Cesarotti, E., Rampino, S., Barone, V.: On the relation between carbonyl stretching frequencies and the donor power of chelating diphosphines in nickel dicarbonyl complexes. Phys. Chem. Chem. Phys. 19, 9028–9038 (2017)

    Google Scholar 

  54. Fusè, M., Rimoldi, I., Facchetti, G., Rampino, S., Barone, V.: Exploiting coordination geometry to selectively predict the \(\sigma \)-donor and \(\pi \)-acceptor abilities of ligands: a back-and-forth journey between electronic properties and spectroscopy. Chem. Commun. 54, 2397–2400 (2018)

    Google Scholar 

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Authors and Affiliations

  1. Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy

    Surajit Nandi, Danilo Calderini, Julien Bloino, Sergio Rampino & Vincenzo Barone

Authors
  1. Surajit Nandi
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  2. Danilo Calderini
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  3. Julien Bloino
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  4. Sergio Rampino
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  5. Vincenzo Barone
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Corresponding author

Correspondence to Sergio Rampino .

Editor information

Editors and Affiliations

  1. Covenant University, Ota, Nigeria

    Sanjay Misra

  2. University of Perugia, Perugia, Italy

    Osvaldo Gervasi

  3. University of Basilicata, Potenza, Italy

    Beniamino Murgante

  4. Saint Petersburg State University, Saint Petersburg, Russia

    Elena Stankova

  5. Saint Petersburg State University, Saint Petersburg, Russia

    Vladimir Korkhov

  6. Polytechnic University of Bari, Bari, Italy

    Carmelo Torre

  7. University of Minho, Braga, Portugal

    Ana Maria A.C. Rocha

  8. Monash University, Clayton, VIC, Australia

    David Taniar

  9. Kyushu Sangyo University, Fukuoka, Japan

    Bernady O. Apduhan

  10. Polytechnic University of Bari, Bari, Italy

    Eufemia Tarantino

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Nandi, S., Calderini, D., Bloino, J., Rampino, S., Barone, V. (2019). A Modern-Fortran Program for Chemical Kinetics on Top of Anharmonic Vibrational Calculations. In: Misra, S., et al. Computational Science and Its Applications – ICCSA 2019. ICCSA 2019. Lecture Notes in Computer Science(), vol 11624. Springer, Cham. https://doi.org/10.1007/978-3-030-24311-1_29

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  • DOI: https://doi.org/10.1007/978-3-030-24311-1_29

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