Abstract
Modeling of structure and properties of molecules and materials (crystals/solids) on the basis of their electronic structure is one of the most important consumers of computer resources (processor time, memory and storage). The known attempts to improve its efficiency reduce to massive parallelization. This approach ignores enormous diversity of types of structures and behaviors of molecules and materials. Moreover, this diversity is by no means reflected in the paradigm currently dominating the field of molecular/material modeling.
Much more efficient is, of course, a thorough analysis of the physical conditions occurring in different molecules/materials. On this way we could successfully build a series of efficient methods targeted upon specific classes of molecules/materials: inorganic ones with open d-shells and organic ones featuring local two-center bonds and developed conjugated \(\uppi \)-systems (generalized chromophores).
The experience gained formulates as a new concept of semi-empirism: that is selecting the electronic wave function of a system under study as a product of the wave functions of the chromophores present in the system. This called for a new development: of a library of objects representing different types of chromophores to be freely combinable to represent an arbitrary molecule/material so that its respective parts (chromophores) are modeled by the most efficient method suitable for the specific type of the chromophore and taking into account the interactions between them. Apparently, the deep segmentation of the system achieved within the new concept of semi-empirism allows for the efficient parallelization and more efficient usage of the HPC software.
Keywords
- New concept of semi-empirism
- Polymorphic trees
- Generalized chromophores
- Cartesius fort library
T-platforms company (Russia) is acknowledged for support extended to the symposium “Quantum Chemical Modeling of Solids with Computers: from Plane Waves to Local Structures (QuaCheSol 2019)” in the frame of the “The 19th International Conference on Computational Science and its Applications (ICCSA 2019)”.
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- 1.
Not in totality seek for unity, rather in uniformity of separation—K. Prutkov.
- 2.
Values must be supplied by metadata including indication to the tensor type of the quantity - \(\mathbb {R}\), \(\mathbb {C}\), \(\mathbb {H}\); rank; space to which the tensor belongs, basis in this space relative to which the quantity is given, units, and mode: whether the quantity is a parameter (input) or result of calculation (output).
References
Nazarian, D., Camp, J.S., Chung, Y.G., Snurr, R.Q., Sholl, D.S.: Chem. Mater. 29, 2521 (2017)
(a) Kresse, G., Hafner, J.: Phys. Rev. B 47 (1993) 558–561; (b) Kresse, G., Furthmüller, J.: Phys. Rev. B 54 (1996) 11169
Gonze, X., et al.: Comput. Phys. Commun. 180, 2582 (2009)
Baroni, S., et al.: J. Phys. Condens. Matt. 29, 465901 (2017)
Zaanen, J., Sawatzky, G.A., Allen, J.: Phys. Rev. Lett. 55, 418 (1985)
Xiang, H., Dronskowski, R., Eck, B., Tchougréeff, A.L.: J. Phys. Chem. A 114, 12345 (2010)
Tchougréeff, A.L., Dronskowski, R.: J. Phys. Chem. A 115, 4547 (2011)
Phung, Q.M., Domingo, A., Pierloot, K.: Chem. Eur. J. 24, 5183 (2018)
Thiel, W.: QM/MM methodology: fundamentals, scope, and limitations in multiscale simulation methods in molecular sciences. In: Grotendorst, J., Attig, N., Blügel, S., Marx, D. (eds.) Institute for Advanced Simulation, Forschungszentrum Jülich, NIC Series, vol. 42, p. 203 (2009)
Tchougréeff, A.L.: Hybrid Methods of Molecular Modeling. Springer, Netherlands (2008). https://doi.org/10.1007/978-1-4020-8189-7
Tchougréeff, A.L.: Khim. Fiz., 16 (1997) No 6, 62. [Chem. Phys. Reports, 16 (1997) 1035]
Tchougréeff, A.L.: Phys. Chem. Chem. Phys. 1, 1051 (1999)
Gasteiger, J., Engel, T. (eds.) Chemoinformatics. Wiley-VCH Verlag GmbH & Co (2003)
Heller, S., McNaught, A., Stein, S., Tchekhovskoi, D., Pletnev, I.: J. Cheminform. 5, 7 (2013)
Heller, S., McNaught, A., Pletnev, I., Stein, S., Tchekhovskoi, D.: J. Cheminform. 7, 23 (2015)
Daudel, R.: In: Pullman, B., Parr, R. (eds.) The New World of Quantum Chemistry, vol. 2, p. 33. Springer, Netherlands (1976). https://doi.org/10.1007/978-94-010-1523-3
McNaught, A.D., Wilkinson, A.: Compendium of Chemical Terminology. The Gold Book, 2nd edn. Blackwell Science, Oxford (1997)
McNaught, A.D., Wilkinson, A.: Compendium of Chemical Terminology. The Gold Book, Version 2.3.3, 24 February 2014
Gordan, P., Alexejeff, V.G.: Z. Phys. Chem. 35, 610 (1900); Alexejeff, V.G.: Z. phys. Chem. 36, 740 (1901)
Tchougréeff, A.L.: Int. J. Quant. Chem. 116, 137 (2016)
Shaik, S., Hiberty, P.C.: A Chemist’s Guide to Valence Bond Theory. Wiley, Hoboken (2007)
Boucher, R., Heller, S., McNaught, A.: Chem. Int. 39, 47 (2017)
“Ferrocene, for instance, may be drawn with the central iron atom connected to each of the two attached rings, to each of the atoms in the rings, to each of the bonds in the rings or not connected at all. The approach taken by InChI is to logically dissociate all atoms capable of forming coordination bonds (metals) and represent the structure as the individual, interconnected components along with the separated, unconnected metal atoms. For a large majority of organometallic compounds, this provides a unique InChI. If a bonded organometallic structure representation is desired, however, it may be specified by adding another series of layers to the InChI.” S.E. Stein, S.R. Heller, D.V. Tchekhovskoi, I.V. Pletnev IUPAC International Chemical Identifier (InChI) InChI version 1, Software version 1.05 Technical Manual. Biomolecular Measurement Division. National Institute of Standards and Technology, Gaithersburg, Maryland, USA. However, this InChI does not necessarily represent adequately their electronic structure: a great advantage of the ‘classical’ structure
Bauerschmidt, S., Gasteiger, J.: J. Chem. Inf. Comput. Sci. 37, 705 (1997)
Witt, O.N.: Ber. Deut. Chem. Ges. 9, 522 (1876)
Ruedenberg, K.: Rev. Mod. Phys. 34, 326 (1962)
Hückel, E.: Z. für Physik 60, 423 (1930); Hückel, E., Hückel, W.: Nature 129, 937 (1932); E. Hückel singled out \(\uppi \)-systems; actually it was clear yet to Pauling and Rumer that in benzene it goes about the description of a collective state of six spins 1/2, but the relation of these spins namely to \(\uppi \)-orbitals
Soudackov, A.V., Tchougréeff, A.L., Misurkin, I.A.: Theor. Chim. Acta 83, 389 (1992)
Harrison, W.A.: Electronic Structure and the Properties of Solids. Freeman, San Francisco (1990)
Bethe, H.A.: Ann. Phys. 3, 133 (1929)
Descartes, R.: Discours de la Méthode, J’ai Lu (2004). (original publication: Imprimerie Ian Meyre a Leyde, 1637)
Lever, A.B.P.: Inorganic Electronic Spectroscopy, 2nd edn. Elsevier, Oxford, Amsterdam, NY (1984)
Tchougréeff, A.L.: Int. J. Quant. Chem. 107, 2519–2538 (2007)
Tchougréeff, A.L., Soudackov, A.V.: Russ. J. Phys. Chem. 88, 1904 (2014)
Tchougréeff, A.L., Soudackov, A.V., van Leusen, J., Kögerler, P., Becker, K.-D., Dronskowski, R.: Int. J. Quant. Chem. 116, 282 (2016)
Tchougréeff, A.L.: J. Struct. Chem. 48, S39 (2007). (in Russian); J. Struct. Chem. 48, S32 (2007). (in English)
Chapman, S.J.: Fortran 95/2003 for Scientists and Engineers, Third Edition The McGraw-Hill Companies, 2008; Intel & #x00AE;Fortran Language Reference. 2003–2005, Intel Corporation; Adams, J.C., Brainerd, W.S., Hendrickson, R.A., Maine, R.E., Martin, J.T., Smith, B.T.: The Fortran 2003 Handbook. The Complete Syntax, Features and Procedures. Springer Science+Business Media (2009)
Languages come and go, paradigms ripe and rot, the whole software business is a part of fashion industry now. But when you want your plane to fly, you still need to do the maths with your trusty Fortran. That’s the beauty of the things that work; they don’t have to change much. https://wordsandbuttons.online/fortran_is_still_a_thing.htm
Popov, I.V., Tchougréeff, A.L.: Comput. Theor. Chem. 1116, 141 (2017)
Popov, I.V., Tchougréeff, A.L.: Theor. Chem. Acc. 138, 9 (2019)
Popov, I.V., Slavin, V.V., Tchougréeff, A.L., Dronskowski, R.: Carbon (Submitted)
NetLaboratory system. https://netlab.cartesius.info/
Acknowledgments
Prof. Dr. I.V. Pletnev (Moscow) is acknowledged for valuable literature indications relative to InChI.
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Tchougréeff, A.L. (2019). cartesius fort - object fortran Library for Chemistry and Materials Science. In: Misra, S., et al. Computational Science and Its Applications – ICCSA 2019. ICCSA 2019. Lecture Notes in Computer Science(), vol 11622. Springer, Cham. https://doi.org/10.1007/978-3-030-24305-0_47
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