Published December 29, 2023 | Version 1.01
Software Open

MarChemSpec (Marine Chemical Speciation Model)

  • 1. University of East Anglia
  • 2. University of Gothenburg
  • 1. ROR icon University of East Anglia
  • 2. ROR icon University of Gothenburg
  • 3. ROR icon Scripps Institution of Oceanography
  • 4. ROR icon Woods Hole Oceanographic Institution

Description

The MarChemSpec Models

These programs (for Windows, Linux, and macOS 'Apple silicon') implement the models described in the three papers, and one manuscript in preparation, listed further below. The models determine the equilibrium chemical speciation for each input natural water composition and temperature. Outputs are the equilibrium composition of the solution on both an amount content and molality basis, all activity coefficients, and other properties as noted below.

The various zip and tar archives contain the executable programs, and functions that can be called by MATLAB or Python.The \docs directory of each archive contains manuals with instructions and examples.

See marchemspec.org for details of our project, and email Simon Clegg (s.clegg@uea.ac.uk) or David Turner (david.turner@marine.gu.se) if you have questions.

1. Models Available as Standalone Programs

Sea - The model of solutions containing the ions of seawater electrolyte (paper 3), including carbonate, borate, and fluoride acid-base equilibria. Outputs include the seawater state parameters alkalinity, pCO2 and fCO2, total and free pH; the stoichiometric acid-base equilibrium constants of carbonate, borate and fluoride; and the stoichiometric concentration product of calcium and carbonate. Estimates of the uncertainties of the calculated quantities are provided.

Delta - This is the same chemical model as 'sea', but calculates the changes in the outputs listed above caused by a change in the natural water composition (typically from seawater to something different). Estimates of the uncertainties of these calculated changes are provided.

Trace - The model of solutions containing the ions of seawater electrolyte, and inorganic complexation of the GEOTRACES metals Al, Cd, Co, Cu(II), Fe(II), Fe(III), Mn, Ni, Pb and Zn (paper 4). Outputs are the concentrations (as amount contents and molalities) of all species, and the free and complexed fractions of each of the trace metals. There are no estimates of uncertainties.

2. MATLAB and Python Functions

These functions, available for Windows and for Linux, allow all three models above to be called directly within MATLAB and Python environments. In addition, the functions include the model of artificial seawater (like seawater electrolyte, but without Sr or carbonate, borate, and fluoride species); and also the draft model of Tris buffer in artificial seawater (papers 1 and 2).

3. Files for Download

Model      Windows                                  Linux                            macOS (Apple silicon)

sea           MarChemSpec_sea.zip              MCS_sea.tar.gz             MCS_sea_macOS.tar.gz

trace         MarChemSpec_delta.zip           MCS_delta.tar.gz           MCS_delta_macOS.tar.gz

delta         MarChemSpec_trace.zip           MCS_trace.tar.gz           MCS_trace_macOS.tar.gz

all             MarChemSpec_MATLAB.zip      MCS_MATLAB.tar.gz                 - 

all             MarChemSpec_Python.zip        MCS_Python.tar.gz                    -

Note: The additional file All_MCS_Manuals.zip contains the manuals and instructions for all models, and it may be helpful to review this first. Windows file MarChemSpec_Excel.zip file contains an Excel worksheet that can be used to run the Sea, Delta, and Trace models (all of which are included in the zip file) on computers running Windows.

4. Papers and Other Documents

1. M. P. Humphreys, J. F. Waters, D. R. Turner, A. G. Dickson, and S. L. Clegg (2022) Chemical speciation models based upon the Pitzer activity coefficient equations, including the propagation of uncertainties: Artificial seawater from 0 to 45 °C. Mar. Chem. 244, art. 104095. https://doi.org/10.1016/j.marchem.2022.104095

2. S. L. Clegg, M. P. Humphreys, J. F. Waters, D. R. Turner, and A. G. Dickson (2022) Chemical speciation models based upon the Pitzer activity coefficient equations, including the propagation of uncertainties. II. Tris buffers in artificial seawater at 25 °C, and an assessment of the seawater 'Total' pH scale. Mar. Chem. 244, art. 104096. https://doi.org/10.1016/j.marchem.2022.104096

3. S. L. Clegg, J. F. Waters, D. R. Turner, and A. G. Dickson (2023) Chemical speciation models based upon the Pitzer activity coefficient equations, including the propagation of uncertainties. III. Seawater from the freezing point to 45 °C, including acid-base equilibria. Mar. Chem. 250, art. 104196. https://doi.org/10.1016/j.marchem.2022.104196

4. The sources and values of equilibrium constants, and Pitzer activity coefficient parameters, are tabulated in the following document available from the authors: D. R. Turner and S. L. Clegg (2023) Sources of Pitzer parameters and equilibrium constants for the GEOTRACES core elements included in the SCOR Working Group 145 chemical speciation model.

A manuscript that describes the trace metal model is in preparation.

 

Notes

Version history

1.00: initial release available only at marchemspec.org (from early June 2023), and used for tutorials at a meeting at Woods Hole Oceanographic Institution during that month. 

1.01: an error in the calculation of activity coefficients of Cu(II) in the 'trace' model at temperatures other than 25 oC has been corrected. Minor improvements were made to the manuals, and in the use of '/' and '\' in path arguments in the Python function. Known issues in this version: (a) an error message related to file handling is incorrect (this should rarely be encountered), (b) there is an error of approx. -0.4% in the calculation of the CO2(g) fugacity coefficient; (c) the speciation calculation fails for some unusual compositions.

Original funding: National Science Foundation (USA), OCE-1744653 and OCE-1744702; and NERC (UK), NE/P012361/1.

Files

All_MCS_Manuals.zip

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Additional details

Related works

References
Journal article: 10.1016/j.marchem.2022.104095 (DOI)
Journal article: 10.1016/j.marchem.2022.104096 (DOI)
Journal article: 10.1016/j.marchem.2022.104196 (DOI)

Funding

NSFGEO-NERC: A Thermodynamic Chemical Speciation Model for the Oceans, Seas, and Estuaries NE/P012361/1
UK Research and Innovation
Collaborative Research: NSFGEO-NERC: A Thermodynamic Chemical Speciation Model for the Oceans, Seas, and Estuaries 1744653
National Science Foundation
Collaborative Research: NSFGEO-NERC: A Thermodynamic Chemical Speciation Model for the Oceans, Seas and Estuaries 1744702
National Science Foundation

Dates

Available
2023-12