Articles | Volume 15, issue 1
Geosci. Model Dev., 15, 15–43, 2022
Geosci. Model Dev., 15, 15–43, 2022
Development and technical paper
04 Jan 2022
Development and technical paper | 04 Jan 2022

PyCO2SYS v1.8: marine carbonate system calculations in Python

Matthew P. Humphreys et al.

Related authors

GLODAPv2.2022: the latest version of the global interior ocean biogeochemical data product
Siv K. Lauvset, Nico Lange, Toste Tanhua, Henry C. Bittig, Are Olsen, Alex Kozyr, Simone R. Alin, Marta Álvarez, Kumiko Azetsu-Scott, Leticia Barbero, Susan Becker, Peter J. Brown, Brendan R. Carter, Leticia Cotrim da Cunha, Richard A. Feely, Mario Hoppema, Matthew P. Humphreys, Masao Ishii, Emil Jeansson, Li-Qing Jiang, Steve D. Jones, Claire Lo Monaco, Akihiko Murata, Jens Daniel Müller, Fiz F. Pérez, Benjamin Pfeil, Carsten Schirnick, Reiner Steinfeldt, Toru Suzuki, Bronte Tilbrook, Adam Ulfsbo, Anton Velo, Ryan J. Woosley, and Robert M. Key
Earth Syst. Sci. Data Discuss.,,, 2022
Preprint under review for ESSD
Short summary
RADIv1: a non-steady-state early diagenetic model for ocean sediments in Julia and MATLAB/GNU Octave
Olivier Sulpis, Matthew P. Humphreys, Monica M. Wilhelmus, Dustin Carroll, William M. Berelson, Dimitris Menemenlis, Jack J. Middelburg, and Jess F. Adkins
Geosci. Model Dev., 15, 2105–2131,,, 2022
Short summary
Dissolution of a submarine carbonate platform by a submerged lake of acidic seawater
Matthew P. Humphreys, Erik H. Meesters, Henk de Haas, Szabina Karancz, Louise Delaigue, Karel Bakker, Gerard Duineveld, Siham de Goeyse, Andreas F. Haas, Furu Mienis, Sharyn Ossebaar, and Fleur C. van Duyl
Biogeosciences, 19, 347–358,,, 2022
Short summary
Norwegian Sea net community production estimated from O2 and prototype CO2 optode measurements on a Seaglider
Luca Possenti, Ingunn Skjelvan, Dariia Atamanchuk, Anders Tengberg, Matthew P. Humphreys, Socratis Loucaides, Liam Fernand, and Jan Kaiser
Ocean Sci., 17, 593–614,,, 2021
Short summary
The pH dependency of the boron isotopic composition of diatom opal (Thalassiosira weissflogii)
Hannah K. Donald, Gavin L. Foster, Nico Fröhberg, George E. A. Swann, Alex J. Poulton, C. Mark Moore, and Matthew P. Humphreys
Biogeosciences, 17, 2825–2837,,, 2020
Short summary

Related subject area

The bulk parameterizations of turbulent air–sea fluxes in NEMO4: the origin of sea surface temperature differences in a global model study
Giulia Bonino, Doroteaciro Iovino, Laurent Brodeau, and Simona Masina
Geosci. Model Dev., 15, 6873–6889,,, 2022
Short summary
NeverWorld2: an idealized model hierarchy to investigate ocean mesoscale eddies across resolutions
Gustavo M. Marques, Nora Loose, Elizabeth Yankovsky, Jacob M. Steinberg, Chiung-Yin Chang, Neeraja Bhamidipati, Alistair Adcroft, Baylor Fox-Kemper, Stephen M. Griffies, Robert W. Hallberg, Malte F. Jansen, Hemant Khatri, and Laure Zanna
Geosci. Model Dev., 15, 6567–6579,,, 2022
Short summary
Observing system simulation experiments reveal that subsurface temperature observations improve estimates of circulation and heat content in a dynamic western boundary current
David E. Gwyther, Colette Kerry, Moninya Roughan, and Shane R. Keating
Geosci. Model Dev., 15, 6541–6565,,, 2022
Short summary
Parallel implementation of the SHYFEM (System of HydrodYnamic Finite Element Modules) model
Giorgio Micaletto, Ivano Barletta, Silvia Mocavero, Ivan Federico, Italo Epicoco, Giorgia Verri, Giovanni Coppini, Pasquale Schiano, Giovanni Aloisio, and Nadia Pinardi
Geosci. Model Dev., 15, 6025–6046,,, 2022
Short summary
Block-structured, equal-workload, multi-grid-nesting interface for the Boussinesq wave model FUNWAVE-TVD (Total Variation Diminishing)
Young-Kwang Choi, Fengyan Shi, Matt Malej, Jane M. Smith, James T. Kirby, and Stephan T. Grilli
Geosci. Model Dev., 15, 5441–5459,,, 2022
Short summary

Cited articles

Abril, G., Bouillon, S., Darchambeau, F., Teodoru, C. R., Marwick, T. R., Tamooh, F., Ochieng Omengo, F., Geeraert, N., Deirmendjian, L., Polsenaere, P., and Borges, A. V.: Technical Note: Large overestimation of pCO2 calculated from pH and alkalinity in acidic, organic-rich freshwaters, Biogeosciences, 12, 67–78,, 2015. a
Álvarez, M., Sanleón-Bartolomé, H., Tanhua, T., Mintrop, L., Luchetta, A., Cantoni, C., Schroeder, K., and Civitarese, G.: The CO2 system in the Mediterranean Sea: a basin wide perspective, Ocean Sci., 10, 69–92,, 2014. a
Bach, L. T.: Reconsidering the role of carbonate ion concentration in calcification by marine organisms, Biogeosciences, 12, 4939–4951,, 2015. a, b
Bakker, D. C. E., Pfeil, B., Landa, C. S., Metzl, N., O'Brien, K. M., Olsen, A., Smith, K., Cosca, C., Harasawa, S., Jones, S. D., Nakaoka, S., Nojiri, Y., Schuster, U., Steinhoff, T., Sweeney, C., Takahashi, T., Tilbrook, B., Wada, C., Wanninkhof, R., Alin, S. R., Balestrini, C. F., Barbero, L., Bates, N. R., Bianchi, A. A., Bonou, F., Boutin, J., Bozec, Y., Burger, E. F., Cai, W.-J., Castle, R. D., Chen, L., Chierici, M., Currie, K., Evans, W., Featherstone, C., Feely, R. A., Fransson, A., Goyet, C., Greenwood, N., Gregor, L., Hankin, S., Hardman-Mountford, N. J., Harlay, J., Hauck, J., Hoppema, M., Humphreys, M. P., Hunt, C. W., Huss, B., Ibánhez, J. S. P., Johannessen, T., Keeling, R., Kitidis, V., Körtzinger, A., Kozyr, A., Krasakopoulou, E., Kuwata, A., Landschützer, P., Lauvset, S. K., Lefèvre, N., Lo Monaco, C., Manke, A., Mathis, J. T., Merlivat, L., Millero, F. J., Monteiro, P. M. S., Munro, D. R., Murata, A., Newberger, T., Omar, A. M., Ono, T., Paterson, K., Pearce, D., Pierrot, D., Robbins, L. L., Saito, S., Salisbury, J., Schlitzer, R., Schneider, B., Schweitzer, R., Sieger, R., Skjelvan, I., Sullivan, K. F., Sutherland, S. C., Sutton, A. J., Tadokoro, K., Telszewski, M., Tuma, M., van Heuven, S. M. A. C., Vandemark, D., Ward, B., Watson, A. J., and Xu, S.: A multi-decade record of high-quality fCO2 data in version 3 of the Surface Ocean CO2 Atlas (SOCAT), Earth Syst. Sci. Data, 8, 383–413,, 2016. a
Bradbury, J., Frostig, R., Hawkins, P., Johnson, M. J., Leary, C., Maclaurin, D., and Wanderman-Milne, S.: JAX: composable transformations of Python+NumPy programs, GitHub, available at: (last access: 23 December 2021), 2018. a
Short summary
The ocean helps to mitigate our impact on Earth's climate by absorbing about a quarter of the carbon dioxide (CO2) released by human activities each year. However, once absorbed, chemical reactions between CO2 and water reduce seawater pH (ocean acidification), which may have adverse effects on marine ecosystems. Our Python package, PyCO2SYS, models the chemical reactions of CO2 in seawater, allowing us to quantify the corresponding changes in pH and related chemical properties.