diff --git a/joss.06536/10.21105.joss.06536.crossref.xml b/joss.06536/10.21105.joss.06536.crossref.xml new file mode 100644 index 0000000000..5ffaeb1705 --- /dev/null +++ b/joss.06536/10.21105.joss.06536.crossref.xml @@ -0,0 +1,267 @@ + + + + 20240529T123511-67f0cb7c07cbda32c7d19ee99f2492d49b6e833c + 20240529123511 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 05 + 2024 + + + 9 + + 97 + + + + PourPy - A python package to generate potential-pH +diagrams + + + + Anja + Korber + + + Fabio E. + Furcas + https://orcid.org/0009-0003-9420-058X + + + Mohit + Pundir + https://orcid.org/0000-0001-7244-7416 + + + David S. + Kammer + https://orcid.org/0000-0003-3782-9368 + + + Ueli M. + Angst + https://orcid.org/0000-0002-2603-4757 + + + + 05 + 29 + 2024 + + + 6536 + + + 10.21105/joss.06536 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.11213255 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/6536 + + + + 10.21105/joss.06536 + https://joss.theoj.org/papers/10.21105/joss.06536 + + + https://joss.theoj.org/papers/10.21105/joss.06536.pdf + + + + + + Atlas d’Équilibres Électrochimiques: Eau +oxygénée + Pourbaix + Centre belge d’étude de la +corrosion + 1963 + Pourbaix, M., & Zoubov, N. de. +(1963). Atlas d’Équilibres Électrochimiques: Eau oxygénée. In Centre +belge d’étude de la corrosion. Paris: +Gauthier-Villars. + + + Commentary: The Materials Project: A +materials genome approach to accelerating materials +innovation + Jain + APL materials + 1 + 1 + 10.1063/1.4812323 + 2013 + Jain, A., Ong, S. P., Hautier, G., +Chen, W., Richards, W. D., Dacek, S., Cholia, S., Gunter, D., Skinner, +D., Ceder, G., & others. (2013). Commentary: The Materials Project: +A materials genome approach to accelerating materials innovation. APL +Materials, 1(1). +https://doi.org/10.1063/1.4812323 + + + SUPCRT92: A software package for calculating +the standard molal thermodynamic properties of minerals, gases, aqueous +species, and reactions from 1 to 5000 bar and 0 to 1000 +C + Johnson + Computers & Geosciences + 7 + 18 + 10.1016/0098-3004(92)90029-Q + 1992 + Johnson, J. W., Oelkers, E. H., & +Helgeson, H. C. (1992). SUPCRT92: A software package for calculating the +standard molal thermodynamic properties of minerals, gases, aqueous +species, and reactions from 1 to 5000 bar and 0 to 1000 C. Computers +& Geosciences, 18(7), 899–947. +https://doi.org/10.1016/0098-3004(92)90029-Q + + + User’s guide to PHREEQC (Version 2): A +computer program for speciation, batch-reaction, one-dimensional +transport, and inverse geochemical calculations + Parkhurst + Water-resources Investigations +Report + 4259 + 99 + 10.3133/wri994259 + 1999 + Parkhurst, D. L., Appelo, C., & +others. (1999). User’s guide to PHREEQC (Version 2): A computer program +for speciation, batch-reaction, one-dimensional transport, and inverse +geochemical calculations. Water-Resources Investigations Report, +99(4259), 312. https://doi.org/10.3133/wri994259 + + + Description of input and examples for PHREEQC +version 3 — a computer program for speciation, batch-reaction, +one-dimensional transport, and inverse geochemical +calculations + Parkhurst + US Geological Survey Techniques and +Methods + A43 + 6 + 10.3133/tm6a43 + 2013 + Parkhurst, D. L., Appelo, C., & +others. (2013). Description of input and examples for PHREEQC version 3 +— a computer program for speciation, batch-reaction, one-dimensional +transport, and inverse geochemical calculations. US Geological Survey +Techniques and Methods, 6(A43), 497. +https://doi.org/10.3133/tm6a43 + + + Introduction to Corrosion +Science + McCafferty + 10.1007/978-1-4419-0455-3 + 1441904549 + 2010 + McCafferty, E. (2010). Introduction +to Corrosion Science [Book]. Springer Science & Business Media. +https://doi.org/10.1007/978-1-4419-0455-3 + + + Corrosion Science and +Engineering + Pedeferri + 720 + 10.1007/978-3-319-97625-9 + 2018 + Pedeferri, P., & Ormellese, M. +(2018). Corrosion Science and Engineering (Vol. 720) [Book]. Springer. +https://doi.org/10.1007/978-3-319-97625-9 + + + Prediction of solid-aqueous equilibria: +Scheme to combine first-principles calculations of solids with +experimental aqueous states + Persson + Phys. Rev. B + 85 + 10.1103/physrevb.85.235438 + 2012 + Persson, K. A., Waldwick, B., Lazic, +P., & Ceder, G. (2012). Prediction of solid-aqueous equilibria: +Scheme to combine first-principles calculations of solids with +experimental aqueous states. Phys. Rev. B, 85, 235438. +https://doi.org/10.1103/physrevb.85.235438 + + + Electrochemical stability of metastable +materials + Singh + Chemistry of Materials + 23 + 29 + 10.1021/acs.chemmater.7b03980 + 2017 + Singh, A. K., Zhou, L., Shinde, A., +Suram, S. K., Montoya, J. H., Winston, D., Gregoire, J. M., & +Persson, K. A. (2017). Electrochemical stability of metastable +materials. Chemistry of Materials, 29(23), 10159–10167. +https://doi.org/10.1021/acs.chemmater.7b03980 + + + The atomic simulation environment — a Python +library for working with atoms + Larsen + Journal of Physics: Condensed +Matter + 27 + 29 + 10.1021/acs.chemmater.7b03980.s001 + 2017 + Larsen, A. H., Mortensen, J. J., +Blomqvist, J., Castelli, I. E., Christensen, R., Dułak, M., Friis, J., +Groves, M. N., Hammer, B., Hargus, C., Hermes, E. D., Jennings, P. C., +Jensen, P. B., Kermode, J., Kitchin, J. R., Kolsbjerg, E. L., Kubal, J., +Kaasbjerg, K., Lysgaard, S., … Jacobsen, K. W. (2017). The atomic +simulation environment — a Python library for working with atoms. +Journal of Physics: Condensed Matter, 29(27), 273002. +https://doi.org/10.1021/acs.chemmater.7b03980.s001 + + + + + + diff --git a/joss.06536/10.21105.joss.06536.pdf b/joss.06536/10.21105.joss.06536.pdf new file mode 100644 index 0000000000..922c89267e Binary files /dev/null and b/joss.06536/10.21105.joss.06536.pdf differ diff --git a/joss.06536/paper.jats/10.21105.joss.06536.jats b/joss.06536/paper.jats/10.21105.joss.06536.jats new file mode 100644 index 0000000000..930f75c259 --- /dev/null +++ b/joss.06536/paper.jats/10.21105.joss.06536.jats @@ -0,0 +1,576 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +6536 +10.21105/joss.06536 + +PourPy - A python package to generate potential-pH +diagrams + + + + +Korber +Anja + +akorber@student.ethz.ch + + + +https://orcid.org/0009-0003-9420-058X + +Furcas +Fabio E. + +ffurcas@ethz.ch + + + +https://orcid.org/0000-0001-7244-7416 + +Pundir +Mohit + +mpundir@ethz.ch + +* + + +https://orcid.org/0000-0003-3782-9368 + +Kammer +David S. + +dkammer@ethz.ch + + + +https://orcid.org/0000-0002-2603-4757 + +Angst +Ueli M. + +uangst@ethz.ch + + + + +Institute for Building Materials, ETH Zrich, +Laura-Hezner-Weg 7, Zrich, 8093, Switzerland + + + + +* E-mail: mpundir@ethz.ch + +9 +97 +6536 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Pourbaix diagrams +thermodynamics +potential +pH + + + + + + Summary +

PourPy is an open-source Python package for + generating thermodynamic stability diagrams of solid phases and + complexes in aqueous electrolytes. These so-called Pourbaix diagrams + provide valuable information about the reactivity of chemical elements + and compounds as a function of the electrochemical potential and the + pH. In the context of corrosion science, environmental and process + engineering, Pourbaix diagrams are useful to predict the reactivity of + aqueous complexes, the passivation behaviour of metals, and the + electrochemical stability of the aqueous electrolyte. + PourPy is a tool enabling users to inspect the + reactivity of aqueous systems under full control of all chemical + species considered. Users can define custom reactive systems + containing multiple solid, aqueous and gaseous species thereof and + build all (electro)chemical reactions to be considered. The package + provides additional functionality to perform basic manipulations on + the thermodynamic parameters associated with each chemical component, + change the system’s reference electrode as well as calculate the + number of phases stable across a given potential-pH space or at + discrete values. Future releases are planned to retrieve thermodynamic + parameters from established databases including SUPCRT92 + (Johnson + et al., 1992) and PHREEQC + (Parkhurst + et al., 1999, + 2013).

+ + + Statement of need +

In 1963, Marcel Pourbaix submitted his PhD thesis titled + Atlas d’Équilibres Électrochimiques, comprising a + collection of thermodynamic equilibrium relationships that describe + the electrochemical stability of chemical elements + (Pedeferri + & Ormellese, 2018; + Pourbaix + & Zoubov, 1963). Over the course of the last century, + graphical representations of these equilibrium relationships, the + so-called Pourbaix diagrams, also known as potential-pH diagrams, have + emerged as an invaluable tool to predict the corrosion bevaviour of + materials. Pourbaix diagrams are widely used in corrosion science to + assess the stability of a metal and its possible different metal + (hydr)oxides + (McCafferty, + 2010). In this context, Pourbaix diagrams provide maps of three + different regions of interest, namely corrosion, + passivity, and immunity. The + corrosion region is the potential-pH domain in which dissolution of + the metal is possible and where it is thermodynamically stable in the + form of dissolved aqueous species. The immunity domain designates the + conditions in which the metal is stable in its unreacted + Me + + 0 + form. Finally, a domain of tremendous technological relevance for many + metals, especially iron-based alloys, is the passivity domain, in + which oxides are stable and can + + – + under some conditions + + – + offer protective properties to the underlying metal. In addition, in + many cases, scales incorporating both metal (hydr)oxide phases and + substances stemming from the exposure environment (carbonate ions, + sulphur species, phosphate species, etc.) can form on the surface as + well and affect the corrosion process. Such cases can also be + investigated by means of Pourbaix diagrams, provided that the relevant + species are incorporated in the thermodynamic calculations carried out + to construct the Pourbaix diagram. While Pourbaix diagrams for simple + cases such as metal-water systems can often be found in the + literature, diagrams for more complex situations or cases deviating + from standard conditions (e.g. in terms of temperature, electrolyte + composition, and/or ionic activity), scholars may face challenges in + obtaining the required Pourbaix diagrams. It should be mentioned here + that Pourbaix diagrams also have limitations. For instance, the + thermodynamically stable phase may not always be the relevant in + practical situations, as intermediates may dominate the behavior over + considerable time scales. Though not energetically favorable, these + intermediate species may also be plotted in the Pourbaix diagram by + excluding other, thermodynamically more stable species and compounds. + Moreover, the lines depicted in Pourbaix diagrams represent the + predominance boundaries, which means that different species / phases + may be stable and present on both sides of these lines. Such + information, although not visible from classical Pourbaix diagrams, + may impact the behavior of the system. Another (well-known) limitation + of Pourbaix diagrams is that they do not provide information on the + kinetics of reactions.

+

Pourbaix diagrams are two-dimensional and Cartesian, plotting the + electrochemical redox potential of e.g. a metal or an alloy versus the + solution pH in contact with the material. Any electrochemical and/or + pH-dependent reaction can be drawn on such a diagram in the form of a + straight line, provided the standard molar Gibbs free energy of + formation + + ΔGf∘ + of all reactants are known. Despite their simplicity and widespread + use in engineering and science, there are few software packages that + generate correct Pourbaix diagrams, without hiding some of their + essential features behind a staggering paywall. Other packages + including pymatgen + (Persson + et al., 2012; + Singh + et al., 2017) part of the The Materials Project + API + (Jain + et al., 2013) and the Atomic Simulation Environment + (ASE) + (Larsen + et al., 2017) are available free of charge, but the diagrams + generated are not customisable and involve DFT modelling methods and + energy minimisation routines far more complicated than the set of + thermodynamic equilibrium relationships originally published. As the + underlying minimisation routines are further performed at each + discrete pH-potential coordinate considered, the generation of + Pourbaix diagrams via the pymatgen or ASE package is also + computationally expensive. PourPy is developed to + address this accessability gap. The package provides a set of seven + classes that handle user-defined chemical reactants and reactions to + be included in a completely customisable Pourbaix diagram. Classes + include functionality to change the reference electrode scale of the + system, control the activity of all aqueous species of a particular + chemical element and interact with the diagram to extract the stable + phase(s) predominant at a given potential and pH coordinate. Lastly, + the provision of a web application eliminates the need to set up a + local installation environment, making the package more accessible to + scholars and engineering professionals.

+ + + Brief software description +

The PourPy package distinguishes between 3 main + line types drawn on the Pourbaix diagram. The first type represents + reactions that are vertical, pH-dependent and involve the exchange of + protons ( + + H+). + The assigned pH can be calculated based on the equilibrium constant of + the chemical reaction. The second type represent potential-dependent + reactions, involving the generation or consumption of electrons + ( + + e−). + They appear as horizontal lines on the diagram. The third archetype of + Pourbaix lines is a combination of the first two, i.e. involving the + exchange of protons and electrons, resulting in a sloped line on the + potential-pH diagram. Consider the formation and consumption of + reactants, products + + Ai, + and protons H+ according to the general chemical reaction + + + ∑iνa,iAi+νH+H+=0, + where + + νa,i + and + + νH+ + are the stoichiometric coefficients of reactants, products and protons + involved. The reaction equilibrium constant + + + β + can be computed from the Gibbs free energy change of the reaction + + + ΔGr∘ + according to + + β=exp(−ΔGr∘/(R⋅T)), + where + + R=8.31446262 + + + Jmol−1K−1 + is the ideal gas constant and + + T + is the temperature in degree K. It also relates to the activity of all + reactants + + K=∏i{Ai}νa,i×{H+}νH+. + Provided the Gibbs free energy of the reaction is known, the pH above + which the formation of products is favoured can be computed as + + + pH=−log10{H+}=1νH+[log10∏i{Ai}νa,i−log10K]. + Reactions that additionally consume or generate electrons (horizontal + or inclined lines), i.e. + + ∑iνa,iAi+νH+H++ne−=0, + are plotted by computing the potential at which the formation of + products becomes favourable via the Nernst Equation + + + Erev=Erev∘+2.303×RTnF×log10∏i{Ai}νa,i+2.303×νH+×RTnF×pH, + where + + n + is the number of electrons transferred and + + + F=96485.3321 + + + Amol−1s−1 + refers to the Faraday constant. For a reaction including the exchange + of protons + + νH+, + Equation 6 corresponds to the third (inclined) line type and for + + + νH+=0, + the second (horizontal) line type is generated. The intersections of + multiple of these line types define regions in the potential-pH space + in which various chemical species + + Ai + are stable. For all + + Ai, + these thermodynamic stability regions are determined based on the sign + of the stoichiometric coefficient + + νa,i, + relative to the stoichiometric coefficients of the protons and + electrons involved in their formation.

+ + + Availability, usage and documentation +

PourPy is written in Python and hosted on + GitLab + and can be accessed via a Mercury-powered + web + application. It has been uploaded to the Python Packaging + Index under the name ‘PourPy’ and can be installed using the + pip + package manager. Users are guided through the functionality + of the package via a set of tutorials available + here. + We encourage collaborative efforts to improve the functionality of + PourPy via the Git repository and appreciate any + suggestions for future features and showcase tutorials.

+ + + Acknowledgements +

The authors thank the European Research Council (ERC) for the + financial support provided for Fabio Enrico Furcas under the European + Union Horizon 2020 research and innovation program (grant agreement + no. 848794).

+ + + Contributions +

F.E.F, D.K. and U.M.A conceived the study, all authors contributed + to the study design. A.K., M.P. and F.E.F. conducted the programming. + F.E.F. wrote the main draft of the manuscript, all authors co-wrote + and approved the final manuscript.

+ + + + + + + + PourbaixM. + ZoubovN. de + + Atlas d’Équilibres Électrochimiques: Eau oxygénée + Paris: Gauthier-Villars + 1963 + + + + + + JainAnubhav + OngShyue Ping + HautierGeoffroy + ChenWei + RichardsWilliam Davidson + DacekStephen + CholiaShreyas + GunterDan + SkinnerDavid + CederGerbrand + others + + Commentary: The Materials Project: A materials genome approach to accelerating materials innovation + APL materials + AIP Publishing + 2013 + 1 + 1 + 10.1063/1.4812323 + + + + + + JohnsonJames W + OelkersEric H + HelgesonHarold C + + SUPCRT92: A software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000 C + Computers & Geosciences + Elsevier + 1992 + 18 + 7 + 10.1016/0098-3004(92)90029-Q + 899 + 947 + + + + + + ParkhurstDavid L + AppeloCAJ + others + + User’s guide to PHREEQC (Version 2): A computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations + Water-resources Investigations Report + 1999 + 99 + 4259 + 10.3133/wri994259 + 312 + + + + + + + ParkhurstDavid L + AppeloCAJ + others + + Description of input and examples for PHREEQC version 3 — a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations + US Geological Survey Techniques and Methods + US Geological Survey Denver, CO, USA + 2013 + 6 + A43 + 10.3133/tm6a43 + 497 + + + + + + + McCaffertyEdward + + Introduction to Corrosion Science + Springer Science & Business Media + 2010 + 1441904549 + 10.1007/978-1-4419-0455-3 + + + + + + PedeferriPietro + OrmelleseMarco + + Corrosion Science and Engineering + Springer + 2018 + 720 + 10.1007/978-3-319-97625-9 + + + + + + PerssonKristin A. + WaldwickBryn + LazicPredrag + CederGerbrand + + Prediction of solid-aqueous equilibria: Scheme to combine first-principles calculations of solids with experimental aqueous states + Phys. Rev. B + American Physical Society + 2012 + 85 + 10.1103/physrevb.85.235438 + 235438 + + + + + + + SinghArunima K + ZhouLan + ShindeAniketa + SuramSantosh K + MontoyaJoseph H + WinstonDonald + GregoireJohn M + PerssonKristin A + + Electrochemical stability of metastable materials + Chemistry of Materials + ACS Publications + 2017 + 29 + 23 + 10.1021/acs.chemmater.7b03980 + 10159 + 10167 + + + + + + LarsenAsk Hjorth + MortensenJens Jørgen + BlomqvistJakob + CastelliIvano E + ChristensenRune + DułakMarcin + FriisJesper + GrovesMichael N + HammerBjørk + HargusCory + HermesEric D + JenningsPaul C + JensenPeter Bjerre + KermodeJames + KitchinJohn R + KolsbjergEsben Leonhard + KubalJoseph + KaasbjergKristen + LysgaardSteen + MaronssonJón Bergmann + MaxsonTristan + OlsenThomas + PastewkaLars + PetersonAndrew + RostgaardCarsten + SchiøtzJakob + SchüttOle + StrangeMikkel + ThygesenKristian S + VeggeTejs + VilhelmsenLasse + WalterMichael + ZengZhenhua + JacobsenKarsten W + + The atomic simulation environment — a Python library for working with atoms + Journal of Physics: Condensed Matter + IOP Publishing + 2017 + 29 + 27 + 10.1021/acs.chemmater.7b03980.s001 + 273002 + + + + + +