Chemical Speciation Modelling Software Now Available for Download

For all potential users of the MarChemSpec models, especially attendees (both in-person and virtual) at the Tutorial and Launch event at Woods Hole on 15th and 16th June: Downloads of the standalone models for execution from a command prompt (and from Excel, for Windows only), and MATLAB and Python functions, are available for Windows and Linux (and now Apple macOS) at the links below.

Attendees at the Tutorials: you will receive an email with some further instructions about what we would like you to do.

These are the programs and functions that can be downloaded:

• The standalone seawater model (MCS_sea): calculate seawater state parameters  (pCO₂, fCO₂, total pH, carbonate and borate equilibrium constants), with estimated uncertainties, for natural waters containing the species of reference seawater but of arbitrary composition.
• The standalone seawater model for the effects of composition change (MCS_delta): calculate the change in seawater state parameters, with estimated uncertainties, corresponding to a change in natural water composition (typically from reference seawater to something with a different major ion composition).
• The standalone model for the calculation of the inorganic complexation of GEOTRACES trace metals (MCS_trace) in natural waters containing the species of seawater but of arbitrary composition.
• MATLAB and Python functions that can carry out several different types of calculation using the seawater and trace metal complexation models (and also one for artificial seawater and Tris buffers).

Functions for the R language will be available later this year.

The downloads are in the form of zip files (Windows) and zipped tar files (Linux and macOS):

• Standalone programs (Windows)
• Standalone programs (Linux)
• Standalone programs (Apple macOS)
• MATLAB and Python functions (Windows)
• MATLAB and Python functions (Linux)
• Standalone programs used from Excel worksheet (Windows)

Questions and comments: email Simon Clegg (s.clegg@uea.ac.uk) for general matters, David Turner (david.turner@marine.gu.se) for MATLAB issues, and Terra Ganey (tganey@ucsc.edu) for Python.

Below: Previous MarChemSpec announcement, with further details

“MARCHEMSPEC” stands for Marine Chemical Speciation, and will be the name for the models and software tools produced by our project. The software implements  our models of natural waters containing the ions of seawater, artificial seawater, and traces metals including the GEOTRACES core species.

The models and software will be launched with talks and demonstrations at Woods Hole Oceanographic Institution, following the June 2023 Ocean Carbon and Biogeochemistry Summer Workshop. These demonstrations, both in-person and online, will take place on Thursday 15th June (afternoon), and Friday the 16th June (morning), US Eastern time.

Please go to this link for more details, and to express your interest in attending. The talks will be recorded. Downloads of the software will be available here (at marchemspec.org) from early June.

These easy-to-use models are for the calculation of: 

• Acid-base equilibria, and CaCO₃ saturation in natural waters containing the ions of seawater.
• Inorganic complexation of trace metals Al, Cd, Co, Cu(II), Fe(II), Fe(III), Mn, Ni, Pb and Zn in natural waters.

What does the software consist of? First, there are two standalone programs that can be run from the command prompt. The first one takes a file of natural water compositions, and temperatures, as input. The outputs are the equilibrium speciation and the calculated values of pH (three different measures), stoichiometric equilibrium constants for the carbonate system, borate, fluoride, and water. These equilibrium constants are expressed on the same basis as those described in, for example, chapter two of Dickson et al. (2007) Guide to Best Practices for Ocean CO₂ Measurements, North Pacific Marine Science Organisation, PICES Special Publication 3, IOCCP Report No. 8. Estimates of uncertainties in the calculated values of these quantities are provided. They are also presented on both an ‘amount content’ basis (moles per kg of solution), and a molality basis (moles per kg of pure water). This is true of all our programs. 

The other standalone program is very similar, except that it takes pairs of natural water compositions as inputs and calculates the changes in pH and the equilibrium constants mentioned above between the two solutions. This program could be used to calculate the change in these key properties associated with a change in composition from that of standard seawater to one with a different ionic composition, for example. The model also provides estimates of the uncertainties in the calculated differences in pH and pK.

These programs are the two most flexible that we can provide, and can easily be used to process large numbers of compositions. Output as .csv files (comma separated values) is provided, and these can be read directly into spreadsheet programs. Current limitations: the compositions of the natural waters are input either as practical salinities or as total amount contents (or molalities) of all solute species, including H⁺. We have not yet added the capability to equilibrate a solution to user-specified values of pairs of the four key variables total pH, alkalinity, DIC, and pCO₂. This will be implemented later in the year.

Second, we have also produced versions of the model that can be called, in a simple way, from within MATLAB, Python, and R. These have essentially the same capabilities as the standalone programs but must be called once for each individual solution being processed. For calculations including trace metals these versions of the model also output the proportions of the total amounts of each dissolved metal that are complexed by each of the inorganic anions.

The software has been developed mostly on Windows machines, which we are most familiar, but should be available for Linux and perhaps for Apple machines by the time of the launch in June. More information will be provided here (and directly, by email, to those who sign up for the presentations and tutorials on the OCB Summer Workshop site.

Simon Clegg (s.clegg@uea.ac.uk) and David Turner (david.turner@marine.gu.se) will give the presentations and demonstrations at the launch event. Please contact one of us if you have questions.

Our colleagues at the National Metrological Institute of Japan, Igor Maksimov and Toshiaki Asakai, have completed a set of Harned Cell measurements of HCl activities in HCl/TrisHCl solutions at different concentrations and temperatures. These data will be used to develop the chemical speciation model of Tris (2-Amino-2-hydroxymethyl-propane-1,3-diol, or THAM) buffers in seawater.They are the first of many sets of similar measurements that will be made in solutions containing Tris, TrisH+, Cl- and the inorganic components of seawater.

We are pleased to announce that Matthew Humphreys, currently working at the National Oceangraphy Centre in Southhampton, will be joining Simon Clegg at UEA. He has been appointed to a 3 year postdoc position to work on the development of the chemical speciation model. He starts work on 1 November 2017.

Matthew is a chemical oceanographer, and his field of study is the marine carbonate system. He did his Ph.D with WG 145 associate member Eric Achterberg.

Matthew’s position is supported by a grant from the Natural Environment Research Council of the UK, which is part of the UK/USA collaboration with WG 145 member Andrew Dickson (whose contribution is supported by the US National Science Foundation).

Simon Clegg has just completed a visit of two and a half months to the University of Gothenburg, Sweden, where he worked with WG 145 Chair David Turner. Experimental work needed for the development of the chemical speciation model was planned, and the current “state of the science” Pitzer model of artificial seawater was assembled and the parameters checked. Our initial goal is to develop a metrologically traceable model of Tris/TrisH+ buffers in artificial seawaters, as a function of both salintiy and temperature. The planned experiments reflect this, and include solutions such as Tris/TrisH+ in NaCl(aq), H+/TrisH+/Cl- solutions, and Tris/TrisH+ in aqueous NaCl/Na2SO4, for example.

The large experimental effort will be shared between Andrew Dickson at Scripps Institution of Oceanography, and our colleagues at the national metrological institutes of Germany, France, and Japan, and at GEOMAR in Kiel (Germany).

We have recently learned of two new/recent projects that, while entirely independent of
our research, are closely related:

• Robert (Bob) Byrne at the University of South Florida, has a three year project entitled “Development of Spectrophotometric pH Measurement Capabilities in Estuaries” (supported by NSF).
• Wei-Jun Cai at the University of Delaware has been funded by NOAA to work on improving scientists’ ability to measure pH in dilute seawater (estuarine environments), and to evaluate the behaviour of different types of electrode. He will be collaborating with scientists at the National Institute of Standards and Technology.

We look forward to exchanging information (and collaborating, if possible) with both Bob and Wei-Jun, beginning with a web-based conference in December 2017.

Following the success of WG 145 members Simon Clegg, Heather Benway, and Andrew Dickson in obtaining 3 year grants from NERC (in the UK) and NSF in the USA, we are very pleased to announce major additions to our collaboration:

• Frank Bastkowski and Steffen Seitz, of Physikalisch-Technische Bundesanstalt (PTB), Braunschweig.
• Igor Maksimov and Toshiaki Asakai, of the National Metrology Institute of Japan.
• Daniela Stoica, of the Laboratoire national de métrologie et d’essai, Paris.
• Pablo Lodeiro and Eric Achterberg, of GEOMAR (the Helmholtz Institute of Ocean Research, Kiel).

The first three groups will all be making Harned Cell measurements of HCl activities in solutions containing Tris/TrisH+ buffer, and the components of seawater (beginning with NaCl).

Pablo and Eric will be measuring salt solubilities in aqueous mixtures, to obtain values of the activities of the salts at saturation. They may also be carrying out potentiometric titrations.

The purpose of both types of experiments is to obtain the activities of dissolved species in the solutions, and so determine the parameters of the Pitzer the chemical speciation model we are developing. These parameters, whose values are functions of temperature and pressure, express the strength of interactions between pairs of cations and anions, and then triplets of ions (two ions of one sign, and one ion of opposite sign). They can only be determined by fitting to measurements.

We and proud to announce that the Natural Environment Environment Council of the UK, and the National Science Foundation in the USA, have awarded a 3 year grant to the project “NSFGEO-NERC: A Thermodynamic Chemical Speciation Model for the Oceans, Seas, and Estuaries“. The investigators on this project are WG  members Simon Clegg (University of East Anglia), Andrew Dickson (Scripps Institution of Oceanography), and Heather Benway (Woods Hole Oceanographic Institution).

Model development will be carried out at UEA, and experiments (using Harned Cells and a calorimeter) at Scripps. Heather, who is the Executive Officer of NSF’s Ocean Carbon and Biogeochemistry  programme, is our link to the chemical oceanography community and will ensure that our efforts meet their needs.