Keywords
Python
markers-in-cell
numeric modeling
petrology
Section
Abstract
Numeric regional models are necessary to reconstruct the nature and conditions of formation of i geological structures, to obtain ideas about the evolution of different zones of the crust and upper mantle, the evolution of fold and fault dislocations and predicting expression of manifestation of deep structures on earth’s surface. Numeric reconstructions are based on computational dynamics methods, in which rock is represented as highly viscous liquid. «Markers-in-cell» method is one of the implementations of that approach. We propose to accelerate model ported into Python, as compared to Matlab, without rejecting sequential enumeration of markers. It is shown that the solutions can be either code vectorization (refactoring with binary indices instead of enumeration loops and numpy functions) or acceleration of loops by their pre-compilation or parallel computations. The results obtained can be used in the implementation of numeric geological modeling in Python.
References
Ивин В.В., Медведев Е.И., Фатьянов И.И. Минералого-геохимическая типизация и зональность многометалльно-серебряного оруденения Нижне-Таежного рудного узла (Северное Приморье) // Успехи современного естествознания. 2018. № 5. С. 76–81 [Ivin V.V., Medvedev E.I., Fatyanov I.I. Mineral-geochemical typesization and zonality of multimetal silver mineralization of the Lower-Taiga ore cluster (Northern Primorye) // Uspekhi sovremennogo yestestvoznaniya. 2018. № 5. P. 76–81 (in Russuan)].
Сахно В.Г., Степанов В.А., Гвоздев В.И., Доброшевский К.Н. Малиновская золоторудная магматическая система Центрального Сихотэ-Алиня: геохронология, петрохимический состав и изотопная характеристика магматических комплексов (Приморье, Россия) // ДАН. 2013. Т. 452. № 1. С. 61–69. https://doi.org/10.7868/s0869565213260174 [Sakhno V.G., Gvozdev V.I., Stepanov V.A. et al. The Malinovka gold-bearing ore-magmatic system of central Sikhote Alin (Primor’e Region, Russia): Geochronology, petrogeochemistry, and isotopic signatures of igneous complexes // Doklady Earth Sciences. 2013. V. 452. № 1. P. 887–894. https://doi.org/10.1134/S1028334X13090043].
Степанов В.А., Бельченко Е.Л., Доброшевский К.Н., Гвоздев В.И. Малиновское золоторудное месторождение, Приморский край // Руды и металлы. 2013. № 3. С. 26–34 [Stepanov V.A., Belchenko E.L., Dobroshevsky K.N., Gvozdev V.I. Malinovskoye zolotorudnoye mestorozhdeniye, Primorskiy kray [Malinovskoye gold deposit, Primorsky region] // Rudy i metally. 2013. № 3. P. 26–34 (in Russian)].
Фатьянов И.И., Хомич В.Г., Борискина Н.Г. Скрытая минерально-геохимическая зональность низкосульфидного золото-серебряного оруденения (месторождение Многовершинное, Нижнее Приамурье) // ДАН, 2010. Т. 435, №1. С. 91–95 [Fatyanov I.I., Khomich V.G., Boriskina N.G. Hidden mineralogical and geochemical zonation of low-sulfide gold-silver mineralization (Mnogovershinnoe deposit, Lower Amur area) // Doklady Earth Sciences. 2010. V. 435. № 1. P. 1456–1459. https://doi.org/10.1134/S1028334X10110103].
Хомич В.Г., Борискина Н.Г. Глубинная геодинамика юго-востока России и позиция платиноносных базит-гипербазитовых массивов // Вулканология и сейсмология. 2013. № 5. С. 40–50 [Khomich V.G., Boriskina N.G. The deep geodynamics of Southeast Russia and the setting of platinum-bearing basite-hyperbasite massifs // Journal of Volcanology and Seismology. 2013. V. 7. № 5. P. 328–337. https://doi.org/10.1134/S0742046313040040].
Хомич В.Г., Борискина Н.Г. Предпосылки обнаружения скрытой Au-Mo-(±Cu)-порфировой минерализации в Покровском рудном поле (Гонжинский район, верхнее Приамурье) // Успехи современного естествознания. 2018. № 6. С. 125–130 [Khomich V.G., Boriskina N.G. Prerequisites to finding of a concealed Au-Mo-(±Cu)-porphyry mineralization in the Pokrovkskoe ore field (Gonzha ore area, Upper Amur region) // Uspekhi sovremennogo yestestvoznaniya. 2018. № 6. P. 125–130 (in Russian)].
Шевырев С.Л., Шевырева М.Ж. Моделирование флюидных рудоносных палеосистем с применением средств дистанционного зондирования Земли как новое направление прогнозных исследований // Вестник ВГУ. Серия: Геология. 2016. № 3. С. 80–85 [Shevyrev S.L., Shevyreva M.Z. Simulation of fluid ore-bearing paleosystems with remote sensing of the earth as new direction of prospective researches // Vestnik VGU. Seriya: Geologiya = Proceedings of Voronezh State University. Series: Geology. 2016. № 3. P. 80–85 (in Russian)].
Юшманов Ю.П., Петрищеский А.М. Белогорская интрузивно-купольная структура (Нижнее Приамурье): глубинное строение и рудно-магматическая зональность // Отечественная геология. 2018. № 1. С. 61–67 [Yushmanov Yu.P., Petrishchevsky A.M. Belogorsk intrusive-dome structure (Lower Amur region): deep structure and ore-magmatic zoning // Otechestvennaya Geologiya. 2018. № 1. P. 61–67 (in Russian)].
Anaconda.Org [Электронный ресурс]. URL: https://anaconda.org (дата обращения: 21.07.2023).
Cambridge University Press. Introduction To Numeric Geodynamics. Book’s page [Электронный ресурс]. URL: https://www.cambridge.org/ru/universitypress/subjects/earth-and-environmental-science/structural-geology-tectonics-and-geodynamics/introduction-numerical-geodynamic-modelling-2nd-edition (accessed 20.07.2023).
Cython. C-Extensions for Python [Электронный ресурс]. URL: https://cython.org (accessed 21.07.2023).
Gerya T. Introduction to Numerical Geodynamic Modelling. 2th edn. Cambridge GB: Cambridge University Press, 2019. 454 p.
Gerya T. Introduction to Numerical Geodynamic Modelling. Zürich CH: Swiss Federal University (ETH), 2009. 359 p.
Gerya T.V., Yuen D.A. Characteristics-based marker-in-cell method with conservative finite-differences schemes for modeling geological flows with strongly variable transport properties // Physics of the Earth and Planetary Interiors. 2003. V. 140. № 4. P. 293–318. https://doi.org/10.1016/j.pepi.2003.09.006
Goudarzi M., Gerya T., van Dinther Y. A comparative analysis of continuum plasticity, viscoplacticity and phase-field models for earthquake sequence modeling // Computational Mechanics. 2023. V. 72. P. 615–633. http://dx.doi.org/10.1007/s00466-023-02311-0
Harlow F.H., Welch J.E. Numerical calculation of time-dependent viscous incompressible flow of fluid with a free surface // Physics of Fluids. 1965. V. 8. № 12. P. 2182–2189. http://doi.org/10.1063/1.1761178
Joblib: running Python functions as pipeline jobs [Электронный ресурс]. URL: https://joblib.readthedocs.io (accessed 21.07.2023).
Kaatz L., Schmalholz S.M., Timm J. Numerical Simulations Reproduce Field Observations Showing Transient Weakening During Shear Zone Formation By Diffusion Hydrogen Influx and H2O Inflow // Geochemistry, Geophysics, Geosystems. 2023. V. 24. e2022GC010830. http://dx.doi.org/10.1029/2022GC010830
Koptev A.I., Cloetingh S., Burov E. et al. Long-distance impact of Iceland plume on Norway’s rifted margin. Scientific Reports. 2017. V. 7. № 1. P. 10408. http://dx.doi.org/10.1038/s41598-017-07523-y
Lavecchio A., Thieulot C., Beekman F. et al. Lithosphere erosion and continental breakup: interaction of extension, plume upwelling and melting // Earth and Planetary Sciences Letters. 2017. V. 467. P. 89–98. http://dx.doi.org/10.1016/j.epsl.2017.03.028
Matplotlib. Visualization with Python [Электронный ресурс]. URL: https://matplotlib.org (accessed 21.07.2023).
Mora P., Morra G., Yuen D.A. Model of plate tectonics with the Lattice Boltzmann Method // Artificial Intelligence in Geosciences. 2023. № 4. P. 47–58. https://doi.org/10.1016/j.aiig.2023.03.002
Moulas E., Schmalholz S.M., Podladchikov Yu. et al. Relation between mean stress, thermodynamic, and lithostatic pressure // Journal of Metamorphic Geology. 2018. V. 37. № 1. P. 1–14. http://dx.doi.org/10.1111/jmg.12446
Morra G. Pythonic geodynamics: implementations for fast computing. Switzerland: Springer Cham, 2018. 227 p. https://doi.org/10.1007/978-3-319-55682-6
Numba: A High Performance Pyhton compiler [Электронный ресурс]. URL: https://numba.pydata.org (accessed 21.07.2023).
Numpy [Электронный ресурс]. URL: https://numpy.org (accessed 21.07.2023).
Python Vs R: Know The Difference [Электронный ресурс]. URL: https://www.interviewbit.com/blog/python-vs-r (accessed 17.07.2023).
Scmitt A.K., Sliwinski J.S., Caricchi L. et al. Zircon age spectra to quantify magma evolution // Geosphere. 2023. V. 19. № 4. P. 1006–1031. https://doi.org/10.1130/GES02563.1
Seif G. Here’s how to use CuPy to make Numpy Over 10X faster [Электронный ресурс]. URL: https://towardsdatascience.com/heres-how-to-use-cupy-to-make-numpy-700x-faster-4b920dda1f56 (accessed 15.06.2023).
Shevyrev S. pyMIC testing repository [Электронный ресурс]. URL: https://github.com/SergeiShevyrev/SergeiShevyrev/tree/main/pyMIC (accessed 08.02.2023).
Shi Y., Wei D., Li Zhong-Hai et al. Subduction Mode Selection During Slab and Mantle Transition Zone Interaction: Numerical Modeling // Pure and Applied Geophysics. 2018. V. 175. P. 529–548. https://link.springer.com/article/10.1007/s00024-017-1762-0
Van Zelst I., Thieulot C., Craig T.J. The effect of temperature-dependent material properties on simple thermal models of subduction zones // Solid Earth. 2023. V. 14. № 7. P. 683–707. http://doi.org/10.5194/se-14-683-2023
Zhong Xinyi, Li Zhong-Hai. Compression at strike-slip fault is a favorable condition for subduction initiation // Geophysical Research Letters. 2023. V. 50. e2022GL102171. http://dx.doi.org/10.1029/2022GL102171
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Copyright (c) 2024 C.Л. Шевырев, Н.Г. Борискина