PyCO2SYS v1.8: marine carbonate system calculations in Python

Oceanic dissolved inorganic carbon (TC) is the largest pool of carbon that substantially interacts with the atmosphere on human timescales. Oceanic TC is increasing through uptake of anthropogenic carbon dioxide (CO2), and seawater pH is decreasing as a consequence. Both the exchange of CO2 between the ocean and atmosphere and the pH response are governed by a set of parameters that interact through chemical equilibria, collectively known as the marine carbonate system. To investigate these processes, at least two of the marine carbonate system's parameters are typically measured – most commonly, two from TC, total alkalinity (AT), pH, and seawater CO2 fugacity (fCO2; or its partial pressure, pCO2, or its dry-air mole fraction, xCO2) – from which the remaining parameters can be calculated and the equilibrium state of seawater solved. Several software tools exist to carry out these calculations, but no fully functional and rigorously validated tool written in Python, a popular scientific programming language, was previously available. Here, we present PyCO2SYS, a Python package intended to fill this capability gap. We describe the elements of PyCO2SYS that have been inherited from the existing CO2SYS family of software and explain subsequent adjustments and improvements. For example, PyCO2SYS uses automatic differentiation to solve the marine carbonate system and calculate chemical buffer factors, ensuring that the effect of every modelled solute and reaction is accurately included in all its results. We validate PyCO2SYS with internal consistency tests and comparisons against other software, showing that PyCO2SYS produces results that are either virtually identical or different for known reasons, with the differences negligible for all practical purposes. We discuss insights that guided the development of PyCO2SYS: for example, the fact that the marine carbonate system cannot be unambiguously solved from certain pairs of parameters. Finally, we consider potential future developments to PyCO2SYS and discuss the outlook for this and other software for solving the marine carbonate system. The code for PyCO2SYS is distributed via GitHub (https://github.com/mvdh7/PyCO2SYS, last access: 23 December 2021) under the GNU General Public License v3, archived on Zenodo (Humphreys et al., 2021), and documented online (https://pyco2sys.readthedocs.io/en/latest/, last access: 23 December 2021).

Pemodelan Sistem Karbonat di Laut Jawa

<p class="Papertext"><strong>Modeling Carbonate System in the Java Sea</strong>. Besides the global fossil fuel burning activities, forest fires in Kalimantan could potentially increase atmospheric CO₂ concentrations, impacting air-sea CO₂ gas exchange in the Java Sea and changing the balance of the marine carbonate system. This study uses a marine carbonate model to examine the processes that control CO₂ flux in the Java Sea and their relationship to CO₂ increase in the atmosphere. OCMIP-2 (<em>Ocean Carbon-Cycle Model Intercomparison Model Project, Phase-2</em>) is performed in this marine carbonate model coupled with the marine ecosystem model. The model results show that the quantity of carbon air flux differs during February and October 2000. More considerable flux is produced during February 2000, where the wind speeds are higher than in October 2000. However, the wind speeds have less impact when the CO₂ level in the atmosphere rises significantly. Due to the influence of a relatively high surface temperature in the tropical Java sea, the Java Sea functions as a carbon source to the atmosphere in general. In this case, the role of the <em>solubility pump</em> is more significant than that of biological processes in carbon absorption. Moreover, increased CO₂ in the atmosphere could alter the partial pressure equilibrium. In the case of 2002 forest fires (atmospheric CO₂ = 460 ppm), the carbon source of the Java Sea was less than before forest fires and even became carbon sink when atmospheric CO₂ rose to 1135.2 ppm based on the highest SSP scenario in 2100. This modeling also reveals marine acidification issues and could rapidly assess the future changes in marine ecosystems due to CO₂ levels rising in the atmosphere.</p>

Geochemistry of natural gases from sediments of terrigenous and carbonate formations of the Bukhara-Khiva oil and gas region of Uzbekistan

The results of long-term studies of natural gases in the Bukhara-Khiva oil and gas region of Uzbekistan are summarized. The results of studying the composition of gases in hydrocarbon deposits generated by OM of continental (terrigenous deposits of the Cretaceous and Middle Jurassic) and marine (carbonate Jurassic) facies are presented. Regularities of changes in individual constituents of gases (hydrocarbons, hydrogen sulfide, carbon dioxide, nitrogen, etc.) with depth are considered; the influence exerted on the composition of gases by various factors and, above all, those of them, which, in the opinion of most researchers, are the main ones. The revealed patterns are used for predictive assessment of the distribution of various constituents of natural gases in the study area.

Genetic Mechanism and Environment Implications of Siderites in the Lopingian Coal-Bearing Series, Western Guizhou of China: Constrained by Whole-Rock and In Situ Geochemistry

A large number of siderites have been found in the Lopingian (Late Permian) coal-bearing series in western Guizhou, which occurs in various microscopic morphologies and has potential insights into the sedimentary and diagenetic environments. An integrated set of analyses, such as microscopic observation; X-ray diffraction; whole-rock major and trace element, carbon, and oxygen isotope; and in situ major and trace element, has been carried out to unravel the genetic mechanism of the siderites and their environmental implications. According to the microscopic morphology, the siderites can be generally divided into three types and six subtypes, including gelatinous siderites (I), microcrystal-silty siderite [II; microlite siderites (II1), powder crystal siderites (II2)], and spheroidal siderite [III, petal-like siderite (III1), radiating fibrous siderite (III2) and concentric siderite (III3)]. Whole-rock geochemical results show that the iron source for the formation of the siderites was mainly from extensive weathering of the Emeishan high-titanium basalts in hot climate conditions. The carbon and oxygen isotopic results indicate that the origin of CO2 in type I siderites is derived from the dehydroxylation of organic matter. The CO2 in types II1 and II2 siderites is mainly derived from deposited organic matter and marine carbonate rocks, respectively. The CO2 source of type III siderites is sedimentary organic matter and marine carbonate rocks and is affected by different fluids during diagenesis. The whole-rock and in situ geochemical characteristics further point to that type I siderites were formed in the synsedimentary period most strongly affected by seawater. Redox proxies, such as V/Sc, V/(V+Ni), and δ Ce, constrained their formation in a stable and weakly reduced condition. Type II siderites could have been developed in saltwater. Among them, type II1 siderites were formed in the early diagenetic stage, whereas type II2 siderites originated from recrystallization of type II1 siderites and accompanied by metasomatism with calcites under diagenetic fluids of weak reduction to weak oxidation conditions. Type III siderites were formed under the influence of multistage diagenetic fluids. Among them, type III1 siderites formed by the growth of powder crystal siderites (II2) under diagenetic fluids with a weak reducing condition. Type III2 siderites formed by growth around microlite siderites under weak reducing diagenetic fluids. Type III3 siderites formed by concentric growth in diagenetic fluids with weak reduction to weak oxidation conditions and relatively active conditions.

In situ stress characteristics of the NE Sichuan basin based on acoustic emission test and imaging logging

This study presents the distribution rule of in situ stress in the northeast Sichuan basin and its relationship with fracture. Sixty-seven sets of core samples of 21 Wells from the terrigenous clastic rock formation (Shaximiao, Qianfoya, Xujiahe) and marine carbonate formation (Jialingjiang, Leikoupo, Feixianguan) in the northeast Sichuan basin were tested by acoustic emission experiment. The in situ stress variation with the depth was established and the corresponding regression analysis was done. The horizontal principal stress direction of terrigenous clastic rock formation and marine carbonate rock formation was obtained by combining the dual diameter data of 6 wells and the imaging logging data of 3 wells. The results show that the vertical stress in the northeast of Sichuan basin has a linear relationship with the depth, and there is little difference between the vertical stress and the overburden weight of rocks. The maximum and minimum horizontal principal stress and horizontal shear stress increase with the burial depth. The divergence degree of horizontal shear stress with depth greater than 3000 m is greater than that of the stratum smaller than 3000 m. The horizontal stress plays a dominant role in the northeast Sichuan basin. With the increase in depth, the influence of tectonic stress field decreases and the vertical stress increases. Impacted by Dabashan and Qinling plate tectonic movement, the direction of in situ stress in marine carbonate strata is nearly east–west. The direction of maximum horizontal principal stress in terrigenous clastic rock formation is basically northwest–southeast. The imaging logging data show that the fracture direction is consistent with the horizontal principal stress direction, and the present in situ stress direction is favorable to the secondary reconstruction of natural fractures, and the fractures keep good opening. The distribution law of in situ stress in northeast Sichuan basin shows σH > σV > σh, indicating that the fault activity in this area is dominated by strike-slip type, the tectonic stress field is dominated by horizontal tectonic stress, in addition that the stress state is conducive to reverse fault activity.

Ostracods from the Pingyi Basin (Eastern China) and their significance on the K/Pg boundary

The Pingyi Basin is a late Mesozoic to Cenozoic fault basin in East China, containing a good record of Cretaceous to Paleogene non-marine carbonate and gypsum deposits. Abundant microfossils including gastropods, ostracods, charophytes and palynomorphs have been reported from this basin. A taxonomic study of ostracods from the Gejiazhuang section in the Pingyi Basin reveals a total of 17 species assigned to 11 genera. A further ostracod biostratigraphic correlation suggests the K/Pg boundary within Member 1 of the Bianqiao Formation in the Gejiazhuang section, which is supported by charophyte biostratigraphic results.