{
  "_id": "6a1f27d6b401979e73422eac",
  "Date": "2026-06-02",
  "Package": "CHNOSZ",
  "Version": "2.2.0-33",
  "Title": "Thermodynamic Calculations and Diagrams for Geochemistry",
  "Authors@R": "c(\nperson(\"Jeffrey\", \"Dick\", , \"j3ffdick@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0687-5890\"))\n)",
  "Author": "Jeffrey Dick [aut, cre] (0000-0002-0687-5890)",
  "Maintainer": "Jeffrey Dick <j3ffdick@gmail.com>",
  "Description": "An integrated set of tools for thermodynamic calculations\nin aqueous geochemistry and geobiochemistry. Functions are\nprovided for writing balanced reactions to form species from\nuser-selected basis species and for calculating the standard\nmolal properties of species and reactions, including the\nstandard Gibbs energy and equilibrium constant. Calculations of\nthe non-equilibrium chemical affinity and equilibrium chemical\nactivity of species can be portrayed on diagrams as a function\nof temperature, pressure, or activity of basis species; in two\ndimensions, this gives a maximum affinity or predominance\ndiagram. The diagrams have formatted chemical formulas and axis\nlabels, and water stability limits can be added to Eh-pH,\noxygen fugacity- temperature, and other diagrams with a redox\nvariable. The package has been developed to handle common\ncalculations in aqueous geochemistry, such as solubility due to\ncomplexation of metal ions, mineral buffers of redox or pH, and\nchanging the basis species across a diagram (\"mosaic\ndiagrams\"). CHNOSZ also implements a group additivity algorithm\nfor the standard thermodynamic properties of proteins.",
  "Encoding": "UTF-8",
  "License": "GPL-3",
  "VignetteBuilder": "knitr",
  "URL": "https://chnosz.net/,\nhttps://r-forge.r-project.org/projects/chnosz/",
  "Repository": "https://r-forge.r-universe.dev",
  "Date/Publication": "2026-06-02 12:33:23 UTC",
  "RemoteUrl": "https://github.com/r-forge/chnosz",
  "RemoteRef": "HEAD",
  "RemoteSha": "76f1ac4022b60d925c33da0c9f2d402ef1f60241",
  "RemoteSubdir": "pkg/CHNOSZ",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-02 18:49:49 UTC",
    "User": "root"
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  "MD5sum": "5f8622da72f0f400e334cc888bee1f6f",
  "_user": "r-forge",
  "_type": "src",
  "_file": "CHNOSZ_2.2.0-33.tar.gz",
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  "_created": "2026-06-02T18:49:49.000Z",
  "_published": "2026-06-05T06:21:36.643Z",
  "_distro": "noble",
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  "_upstream": "https://github.com/r-forge/chnosz",
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    "author": "jedick (Jeffrey Dick) <j3ffdick@gmail.com>",
    "committer": "jedick (Jeffrey Dick) <j3ffdick@gmail.com>",
    "message": "Add FAQ: How is sum of activities defined for mosaic()?\n\n\ngit-svn-id: svn://svn.r-forge.r-project.org/svnroot/chnosz@966 edb9625f-4e0d-4859-8d74-9fd3b1da38cb\n",
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    "name": "Jeffrey Dick",
    "email": "j3ffdick@gmail.com",
    "login": "jedick",
    "linkedin": "in/jeffrey-m-dick",
    "description": "Research data scientist | Genomics | Geochemistry | R - Python - NLP - GenAI",
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    "orcid": "0000-0002-0687-5890"
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  "_owner": "r-forge",
  "_selfowned": true,
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  "_contributors": [
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    "name": " R-Forge",
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  "_downloads": {
    "count": 944,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CHNOSZ"
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  "_mentions": 13,
  "_devurl": "https://github.com/r-forge/chnosz",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/r-forge/chnosz",
  "_realowner": "r-forge",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.8",
      "date": "2009-04-23"
    },
    {
      "version": "0.9",
      "date": "2009-11-30"
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    {
      "version": "0.9-1",
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      "date": "2011-04-05"
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    {
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    },
    {
      "version": "0.9-7",
      "date": "2011-08-23"
    },
    {
      "version": "0.9-9",
      "date": "2013-01-01"
    },
    {
      "version": "1.0.0",
      "date": "2013-03-28"
    },
    {
      "version": "1.0.1",
      "date": "2013-07-04"
    },
    {
      "version": "1.0.3",
      "date": "2014-01-12"
    },
    {
      "version": "1.0.3.1",
      "date": "2014-02-12"
    },
    {
      "version": "1.0.5",
      "date": "2015-05-19"
    },
    {
      "version": "1.0.6",
      "date": "2015-10-19"
    },
    {
      "version": "1.0.7",
      "date": "2015-11-19"
    },
    {
      "version": "1.0.8",
      "date": "2016-05-28"
    },
    {
      "version": "1.1.0",
      "date": "2017-05-04"
    },
    {
      "version": "1.1.3",
      "date": "2017-11-13"
    },
    {
      "version": "1.2.0",
      "date": "2019-02-10"
    },
    {
      "version": "1.3.0",
      "date": "2019-02-25"
    },
    {
      "version": "1.3.1",
      "date": "2019-03-04"
    },
    {
      "version": "1.3.2",
      "date": "2019-04-21"
    },
    {
      "version": "1.3.3",
      "date": "2019-08-03"
    },
    {
      "version": "1.3.4",
      "date": "2019-12-15"
    },
    {
      "version": "1.3.5",
      "date": "2020-02-17"
    },
    {
      "version": "1.3.6",
      "date": "2020-03-16"
    },
    {
      "version": "1.4.0",
      "date": "2020-11-11"
    },
    {
      "version": "1.4.1",
      "date": "2021-04-09"
    },
    {
      "version": "1.4.2",
      "date": "2022-02-08"
    },
    {
      "version": "1.4.3",
      "date": "2022-02-22"
    },
    {
      "version": "2.0.0",
      "date": "2023-03-13"
    },
    {
      "version": "2.1.0",
      "date": "2024-02-11"
    },
    {
      "version": "2.2.0",
      "date": "2025-06-20"
    }
  ],
  "_exports": [
    "add.OBIGT",
    "add.protein",
    "affinity",
    "allparents",
    "aminoacids",
    "as.chemical.formula",
    "axis.label",
    "basis",
    "basis.elements",
    "basis.logact",
    "Berman",
    "bgamma",
    "calculateDensity",
    "calculateEpsilon",
    "calculateGibbsOfWater",
    "calculateQ",
    "check.EOS",
    "check.GHS",
    "check.OBIGT",
    "CHNOSZ",
    "convert",
    "count.elements",
    "Cp_s_var",
    "describe.basis",
    "describe.property",
    "describe.reaction",
    "diagram",
    "dimSums",
    "dPdTtr",
    "dumpdata",
    "E.units",
    "element.mu",
    "entropy",
    "EOScalc",
    "EOScoeffs",
    "EOSlab",
    "EOSplot",
    "EOSregress",
    "EOSvar",
    "equil.boltzmann",
    "equil.reaction",
    "equilibrate",
    "expr.property",
    "expr.species",
    "expr.units",
    "find.tp",
    "getnames",
    "getnodes",
    "getrank",
    "GHS",
    "GHS_Tr",
    "hyphen.in.pdf",
    "i2A",
    "IAPWS95",
    "ibasis",
    "info",
    "ionize.aa",
    "label.figure",
    "label.plot",
    "list2array",
    "lNaCl",
    "logK.to.OBIGT",
    "lP",
    "lS",
    "lT",
    "lTP",
    "makeup",
    "mash",
    "mass",
    "mix",
    "mod.buffer",
    "mod.OBIGT",
    "moles",
    "mosaic",
    "MP90.cp",
    "mtitle",
    "NaCl",
    "nonideal",
    "OBIGT",
    "P.units",
    "palply",
    "parent",
    "phospho_plot",
    "phosphorylate",
    "pinfo",
    "protein.basis",
    "protein.formula",
    "protein.length",
    "protein.OBIGT",
    "rank.affinity",
    "ratlab",
    "rebalance",
    "reset",
    "retrieve",
    "RH2OBIGT",
    "rho.IAPWS95",
    "sciname",
    "slice",
    "slice.affinity",
    "solubility",
    "species",
    "stack_mosaic",
    "subcrt",
    "swap.basis",
    "syslab",
    "T.units",
    "thermo",
    "thermo.axis",
    "thermo.plot.new",
    "thermo.refs",
    "Ttr",
    "unitize",
    "usrfig",
    "V_s_var",
    "water",
    "water.AW90",
    "water.DEW",
    "water.IAPWS95",
    "water.lines",
    "water.SUPCRT92",
    "which.pmax",
    "WP02.auxiliary",
    "ZC",
    "ZC.col"
  ],
  "_help": [
    {
      "page": "CHNOSZ-package",
      "title": "Thermodynamic calculations and diagrams for geochemistry",
      "topics": [
        "CHNOSZ-package"
      ]
    },
    {
      "page": "add.OBIGT",
      "title": "Functions to Work with the Thermodynamic Database",
      "concept": [
        "Thermodynamic data"
      ],
      "topics": [
        "add.OBIGT",
        "mod.OBIGT"
      ]
    },
    {
      "page": "add.protein",
      "title": "Amino acid compositions of proteins",
      "concept": [
        "Protein properties"
      ],
      "topics": [
        "add.protein"
      ]
    },
    {
      "page": "affinity",
      "title": "Chemical affinities of formation reactions",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "affinity"
      ]
    },
    {
      "page": "basis",
      "title": "Define basis species",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "basis"
      ]
    },
    {
      "page": "Berman",
      "title": "Thermodynamic properties of minerals",
      "concept": [
        "Thermodynamic calculations"
      ],
      "topics": [
        "Berman"
      ]
    },
    {
      "page": "DEW",
      "title": "Deep Earth Water (DEW) model",
      "concept": [
        "Water properties"
      ],
      "topics": [
        "calculateDensity",
        "calculateEpsilon",
        "calculateGibbsOfWater",
        "calculateQ",
        "DEW"
      ]
    },
    {
      "page": "diagram",
      "title": "Chemical activity diagrams",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "diagram",
        "find.tp"
      ]
    },
    {
      "page": "EOSregress",
      "title": "Regress equations-of-state parameters for aqueous species",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "Cp_s_var",
        "EOScalc",
        "EOScoeffs",
        "EOSlab",
        "EOSplot",
        "EOSregress",
        "EOSvar",
        "V_s_var"
      ]
    },
    {
      "page": "equilibrate",
      "title": "Equilibrium chemical activities of species",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "equil.boltzmann",
        "equil.reaction",
        "equilibrate",
        "moles"
      ]
    },
    {
      "page": "examples",
      "title": "Run package examples and demos",
      "concept": [
        "Other tools"
      ],
      "topics": [
        "demos",
        "examples"
      ]
    },
    {
      "page": "extdata",
      "title": "Extra data",
      "concept": [
        "Thermodynamic data"
      ],
      "topics": [
        "extdata"
      ]
    },
    {
      "page": "IAPWS95",
      "title": "Properties of water from IAPWS-95",
      "concept": [
        "Water properties"
      ],
      "topics": [
        "IAPWS95"
      ]
    },
    {
      "page": "info",
      "title": "Search the thermodynamic database",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "info"
      ]
    },
    {
      "page": "ionize.aa",
      "title": "Properties of ionization of proteins",
      "concept": [
        "Protein properties"
      ],
      "topics": [
        "ionize.aa"
      ]
    },
    {
      "page": "logK.to.OBIGT",
      "title": "Fit thermodynamic parameters to formation constants (log K)",
      "topics": [
        "logK.to.OBIGT"
      ]
    },
    {
      "page": "makeup",
      "title": "Parse chemical formulas",
      "concept": [
        "Thermodynamic calculations"
      ],
      "topics": [
        "count.elements",
        "makeup"
      ]
    },
    {
      "page": "mix",
      "title": "Combine diagrams for multi-metal systems",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "mash",
        "mix",
        "rebalance"
      ]
    },
    {
      "page": "mod.buffer",
      "title": "Calculating buffered chemical activities",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "buffer",
        "mod.buffer"
      ]
    },
    {
      "page": "mosaic",
      "title": "Chemical affinities with changing basis species",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "mosaic"
      ]
    },
    {
      "page": "NaCl",
      "title": "Simple NaCl-water solution model",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "NaCl"
      ]
    },
    {
      "page": "nonideal",
      "title": "Activity coefficients of aqueous species",
      "concept": [
        "Thermodynamic calculations"
      ],
      "topics": [
        "bgamma",
        "nonideal"
      ]
    },
    {
      "page": "palply",
      "title": "Conditional parallel processing",
      "concept": [
        "Utility functions"
      ],
      "topics": [
        "palply"
      ]
    },
    {
      "page": "phosphorylate",
      "title": "Calculate affinity of phosphorylation reactions with pH-dependent speciation",
      "concept": [
        "Thermodynamic calculations"
      ],
      "topics": [
        "phosphorylate",
        "phospho_plot"
      ]
    },
    {
      "page": "protein.info",
      "title": "Summaries of thermodynamic properties of proteins",
      "concept": [
        "Protein properties"
      ],
      "topics": [
        "pinfo",
        "protein.basis",
        "protein.formula",
        "protein.info",
        "protein.length",
        "protein.OBIGT"
      ]
    },
    {
      "page": "rank.affinity",
      "title": "Average ranks of chemical affinities",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "rank.affinity"
      ]
    },
    {
      "page": "retrieve",
      "title": "Retrieve species by element",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "retrieve"
      ]
    },
    {
      "page": "solubility",
      "title": "Equilibrium chemical activities of species",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "solubility"
      ]
    },
    {
      "page": "species",
      "title": "Species of interest",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "species"
      ]
    },
    {
      "page": "stack_mosaic",
      "title": "Stacked mosaic diagram",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "stack_mosaic"
      ]
    },
    {
      "page": "subcrt",
      "title": "Properties of species and reactions",
      "concept": [
        "Main workflow"
      ],
      "topics": [
        "subcrt"
      ]
    },
    {
      "page": "swap.basis",
      "title": "Swap basis species",
      "concept": [
        "Extended workflow"
      ],
      "topics": [
        "basis.elements",
        "basis.logact",
        "element.mu",
        "ibasis",
        "swap.basis"
      ]
    },
    {
      "page": "taxonomy",
      "title": "Extract data from NCBI taxonomy files",
      "concept": [
        "Other tools"
      ],
      "topics": [
        "allparents",
        "getnames",
        "getnodes",
        "getrank",
        "parent",
        "sciname",
        "taxonomy"
      ]
    },
    {
      "page": "thermo",
      "title": "Thermodynamic database and system settings",
      "concept": [
        "Thermodynamic data"
      ],
      "topics": [
        "CHNOSZ",
        "OBIGT",
        "reset",
        "thermo"
      ]
    },
    {
      "page": "thermo.plot",
      "title": "Functions to create and modify plots",
      "concept": [
        "Utility functions"
      ],
      "topics": [
        "thermo.axis",
        "thermo.plot",
        "thermo.plot.new"
      ]
    },
    {
      "page": "util.array",
      "title": "Functions to work with multidimensional arrays",
      "concept": [
        "Utility functions"
      ],
      "topics": [
        "dimSums",
        "list2array",
        "slice",
        "slice.affinity",
        "util.array"
      ]
    },
    {
      "page": "util.data",
      "title": "Functions for checking thermodynamic data",
      "concept": [
        "Thermodynamic data"
      ],
      "topics": [
        "check.EOS",
        "check.GHS",
        "check.OBIGT",
        "dumpdata",
        "RH2OBIGT",
        "thermo.refs",
        "util.data"
      ]
    },
    {
      "page": "util.expression",
      "title": "Functions to express chemical formulas and properties",
      "concept": [
        "Utility functions"
      ],
      "topics": [
        "axis.label",
        "describe.basis",
        "describe.property",
        "describe.reaction",
        "expr.property",
        "expr.species",
        "expr.units",
        "ratlab",
        "syslab",
        "util.expression"
      ]
    },
    {
      "page": "util.formula",
      "title": "Functions to work with chemical formulas",
      "concept": [
        "Thermodynamic calculations"
      ],
      "topics": [
        "as.chemical.formula",
        "entropy",
        "GHS",
        "i2A",
        "mass",
        "util.formula",
        "ZC"
      ]
    },
    {
      "page": "util.legend",
      "title": "Functions to make legend text",
      "concept": [
        "Utility functions"
      ],
      "topics": [
        "lNaCl",
        "lP",
        "lS",
        "lT",
        "lTP",
        "util.legend"
      ]
    },
    {
      "page": "util.list",
      "title": "Functions to work with lists",
      "concept": [
        "Utility functions"
      ],
      "topics": [
        "util.list",
        "which.pmax"
      ]
    },
    {
      "page": "util.misc",
      "title": "Functions for miscellaneous tasks",
      "concept": [
        "Thermodynamic calculations"
      ],
      "topics": [
        "dPdTtr",
        "GHS_Tr",
        "Ttr",
        "unitize",
        "util.misc"
      ]
    },
    {
      "page": "util.plot",
      "title": "Utility functions for plots",
      "concept": [
        "Utility functions"
      ],
      "topics": [
        "hyphen.in.pdf",
        "label.figure",
        "label.plot",
        "mtitle",
        "usrfig",
        "util.plot",
        "water.lines",
        "ZC.col"
      ]
    },
    {
      "page": "util.protein",
      "title": "Functions for proteins (other calculations)",
      "concept": [
        "Protein properties"
      ],
      "topics": [
        "group.formulas",
        "MP90.cp",
        "util.protein"
      ]
    },
    {
      "page": "util.seq",
      "title": "Functions to work with sequence data",
      "concept": [
        "Protein properties"
      ],
      "topics": [
        "aminoacids",
        "util.seq"
      ]
    },
    {
      "page": "util.units",
      "title": "Functions to convert units",
      "concept": [
        "Thermodynamic calculations"
      ],
      "topics": [
        "convert",
        "E.units",
        "P.units",
        "T.units",
        "util.units"
      ]
    },
    {
      "page": "util.water",
      "title": "Functions for properties of water and steam",
      "concept": [
        "Water properties"
      ],
      "topics": [
        "rho.IAPWS95",
        "util.water",
        "water.AW90",
        "WP02.auxiliary"
      ]
    },
    {
      "page": "water",
      "title": "Properties of water",
      "concept": [
        "Water properties"
      ],
      "topics": [
        "water",
        "water.DEW",
        "water.IAPWS95",
        "water.SUPCRT92"
      ]
    }
  ],
  "_readme": "https://github.com/r-forge/chnosz/raw/HEAD/pkg/CHNOSZ/README.md",
  "_rundeps": [],
  "_vignettes": [
    {
      "source": "anintro.Rmd",
      "filename": "anintro.html",
      "title": "An Introduction to CHNOSZ",
      "author": "Jeffrey M. Dick",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Getting Started",
        "Basic Functionality",
        "Organization of CHNOSZ",
        "Functions without side effects (return values)",
        "Functions with side effects (modify system state)",
        "Querying the thermodynamic database",
        "Calculating thermodynamic properties",
        "Working with reactions",
        "Chemical affinity and stability diagrams",
        "Equilibrium calculations",
        "Activity coefficients",
        "References",
        "Interlude: Affinity, Formation Reactions, and Balancing",
        "Caution: Quasisolubility contours on predominance diagrams underestimate total solubility",
        "Advanced Uses",
        "1. Use helper functions to create formatted labels for diagrams",
        "2. Use <span style=\"color:green;font-family:monospace;\">retrieve()</span> to search species by elements",
        "3. Load optional data with <span style=\"color:red;font-family:monospace;\">add.OBIGT()</span>",
        "4. Use <span style=\"color:red;font-family:monospace;\">OBIGT()</span> and <span style=\"color:red;font-family:monospace;\">reset()</span> to restore the default database and settings",
        "5. Use <span style=\"color:red;font-family:monospace;\">basis()</span> species to define the compositional space",
        "6. Set activities of formed <span style=\"color:red;font-family:monospace;\">species()</span> to define a quasisolubility contour",
        "7. When to use <span style=\"font-family:monospace;\">add = TRUE</span>",
        "8. Set grid resolution and constant T, P, or ionic strength in <span style=\"color:green;font-family:monospace;\">affinity()</span>",
        "9. Use <span style=\"color:green;font-family:monospace;\">NaCl()</span> to estimate ionic strength from NaCl concentration",
        "10. Use <span style=\"color:green;font-family:monospace;\">solubility()</span> to draw total solubility contours",
        "11. Use <span style=\"color:green;font-family:monospace;\">convert()</span> for common unit conversions",
        "12. Use the transect mode of <span style=\"color:green;font-family:monospace;\">affinity()</span> for synchronized variables",
        "13. Choose non-default balancing constraints in <span style=\"color:green;font-family:monospace;\">diagram()</span>",
        "14. Calculate adjusted and non-standard Gibbs energy with <span style=\"color:green;font-family:monospace;\">subcrt()</span>",
        "15. Calculate non-standard Gibbs energy with <span style=\"color:green;font-family:monospace;\">affinity()</span>",
        "And swap basis species, remove formed species, and label reactions",
        "16. Extract results from the output of <span style=\"color:green;font-family:monospace;\">diagram()</span>",
        "17. Writing chemical formulas and counting and summing elements with <span style=\"color:green;font-family:monospace;\">makeup()</span>",
        "18: Accessing and changing settings with <span style=\"color:red;font-family:monospace;\">thermo()</span>",
        "Interlude: From Activity to Molality",
        "Buffers",
        "1. Defining buffers with <span style=\"color:red;font-family:monospace;\">mod.buffer()</span>",
        "2. Retrieving buffered activities with <span style=\"color:green;font-family:monospace;\">affinity(return.buffer = TRUE)</span>",
        "3. Working with multiple buffered species (e.g., r h2s and r o2 in PPM)",
        "4. Using <span style=\"color:green;font-family:monospace;\">diagram(type = )</span> to display buffered activities",
        "5. Using fr o2 Buffers in downstream calculations",
        "6. Using buffer calculations in transects with <span style=\"color:green;font-family:monospace;\">affinity()</span>",
        "7. Calculating the neutral pH of water",
        "8. Working with mineral pH buffers",
        "Comprehensive example: Ore formation environments",
        "Proteins",
        "1. Identifying proteins",
        "2. Adding proteins from FASTA or CSV files",
        "3. Calculating protein properties",
        "Protein length and formula",
        "Carbon oxidation state",
        "4. Thermodynamic calculations for proteins",
        "Standard thermodynamic properties",
        "Ionization effects",
        "5. Setting up a chemical system with proteins",
        "6. Calculating affinities and equilibrium distributions",
        "Affinities of formation reactions",
        "Equilibrium distributions",
        "Scaling protein abundances",
        "7. Additional protein analysis",
        "End-to-end example: Parameter optimization to fit experimental protein abundances",
        "Environmental controls on protein evolution: A case study with CRISPR-Cas systems",
        "Further Resources - Demos",
        "More use cases for <span style=\"color:green;font-family:monospace;\">mosaic()</span>",
        "Solubility contours with <span style=\"color:green;font-family:monospace;\">solubility()</span>",
        "Other contour plots",
        "Calculations using the output of <span style=\"color:green;font-family:monospace;\">diagram()</span>",
        "Activity buffers",
        "Other thermodynamic models",
        "Calculations with proteins",
        "Further Resources - Vignettes",
        "Frequently asked questions",
        "OBIGT thermodynamic database",
        "Customizing the thermodynamic database",
        "Fitting thermodynamic data",
        "Creating multi-metal diagrams",
        "Getting Help",
        "Document History"
      ],
      "created": "2017-02-04 12:55:30",
      "modified": "2026-06-02 12:33:23",
      "commits": 215
    },
    {
      "source": "FAQ.Rmd",
      "filename": "FAQ.html",
      "title": "CHNOSZ FAQ",
      "author": "Jeffrey M. Dick",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How is CHNOSZ pronounced?",
        "Where do the names CHNOSZ, OBIGT, and subcrt come from?",
        "How should CHNOSZ be cited?",
        "What thermodynamic models are used in CHNOSZ?",
        "What are the main limitations of CHNOSZ?",
        "When and why do equal-activity boundaries depend on total activity?",
        "Set up subplots",
        "Activate DEW model",
        "logfO2-pH diagram for aqueous inorganic and organic carbon species at high pressure",
        "After Figure 1b of Sverjensky et al., 2014b [SSH14]",
        "(Nature Geoscience, https://doi.org/10.1038/NGEO2291)",
        "Define system",
        "A function to make the diagrams",
        "Set total C concentration to 0.03 molal",
        "(from EQ3NR model for eclogite [Supporting Information of SSH14])",
        "Restore default settings for the questions below",
        "How can minerals with polymorphic transitions be added to the database?",
        "How can I make a diagram with the trisulfur radical ion (r S3minus)?",
        "Why does the published diagram have a much larger stability field for r S3minus?",
        "Can I make the diagram using the Deep Earth Water (DEW) model?",
        "In OBIGT, what is the meaning of T for solids, liquids, and gases?",
        "How can mineral pH buffers be plotted?",
        "Why are mineral stability boundaries curved on mosaic diagrams?",
        "Get the pKa of H2S (note the minus sign!)",
        "Reaction 1 between pyrite and pyrrhotite with H2S",
        "Reaction 1 law of mass action (LMA)",
        "logf_O2 = 2 logK_1 - 2 loga_H2S",
        "Reaction 2 between pyrite and pyrrhotite with HS-",
        "Reaction 2 LMA",
        "logf_O2 = 2 pH + 2 logK_2 - 2 loga_HS-",
        "The logf_O2 for each reaction is the same at the pKa of H2S",
        "How is the sum of activities of basis species defined for mosaic diagrams?",
        "The basis species we are speciating",
        "The basis species defining the system",
        "Note 1: for mosaic(), the first species in 'bases' must be in this list",
        "Note 2: for solubility(), the first species in this list must contain S",
        "Define a low fO2 so reduced sulfur dominates over most of the pH range",
        "The pH range we'll look at",
        "The logarithm of activity used for aH2S or sum(S)",
        "Left-hand plot: Constant log aH2S, variable sum(S)",
        "Set it up as a solubility calculation",
        "Define a single log aH2S",
        "Specify the aqueous species in equilibrium with H2S",
        "Run the calculation to calculate all species' activities",
        "Diagram individual activities then total activity",
        "Right-hand plot: Constant sum(S), variable log aH2S",
        "Start by loading all the candidate species with preset activities",
        "Calculate affinities of formation reactions",
        "Equilibrate the species for a total activity of S",
        "Look at the stabilities of calcite and anhydrite",
        "For afffinity(), these are single activities",
        "For mosaic(), these are total activities for groups of species in the 'bases' list",
        "affinity() calculation",
        "mosaic() calculation",
        "References"
      ],
      "created": "2023-05-17 08:54:57",
      "modified": "2026-06-02 12:33:23",
      "commits": 38
    },
    {
      "source": "custom_data.Rmd",
      "filename": "custom_data.html",
      "title": "Customizing the thermodynamic database",
      "author": "Jeffrey M. Dick",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Basic structure of OBIGT",
        "Conventions for data entry in OBIGT",
        "Types of data",
        "Ranges of HKF and CGL models",
        "Required and optional data",
        "NA or 0?",
        "OOM scaling and r info_",
        "Case study: NA and 0 in the default database",
        "Examples of adding data from a file",
        "r add.OBIGT_ with optional data files",
        "r add.OBIGT_ with other CSV files",
        "Examples of adding and modifying data with a function",
        "r mod.OBIGT_ for aqueous species",
        "r mod.OBIGT_ for minerals",
        "Case study: Formation constants for aqueous tungsten species",
        "Fitting formation constants",
        "Diagram 1: Constant molality of r F_",
        "Diagram 2: Variable molality of r F_",
        "References"
      ],
      "created": "2023-03-03 04:56:39",
      "modified": "2025-06-02 09:14:27",
      "commits": 11
    },
    {
      "source": "multi-metal.Rmd",
      "filename": "multi-metal.html",
      "title": "Diagrams with multiple metals",
      "author": "Jeffrey M. Dick",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Mashing",
        "Mixing 1",
        "Convert formation energies from eV / atom to eV / molecule",
        "Convert formation energies from eV / molecule to J / mol",
        "Gibbs energies of formation (J / mol) for aqueous species",
        "Most are from Wagman et al., 1982",
        "Gibbs energies of formation (J / mol) for solids from Wagman et al., 1982",
        "Calculate correction for difference between reference and DFT energies (Persson et al., 2012)",
        "Apply correction to standard Gibbs energies of aqueous species (Persson et al., 2012)",
        "Add energies to OBIGT",
        "This function modifies OBIGT and returns the species indices of the affected species",
        "We explicitly set the units to Joules (this is the default as of CHNOSZ 2.0.0)",
        "We need model = \"CGL\" to override the Berman model for some minerals 20220919",
        "Formation energies (eV / atom) for bimetallic solids from Materials API",
        "mp-1335, mp-1079399, mp-866134, mp-558525, mp-504509 (triclinic FeVO4)",
        "Convert energies and add to OBIGT",
        "Mosaic Stacking 1",
        "Mosaic Stacking 2",
        "Setup basis species",
        "Fe-bearing minerals",
        "Add aqueous species 20210220",
        "Start plot with just the fields for transparency effect",
        "Cu-bearing minerals",
        "Mosaic with all Fe species as basis species",
        "Use only predominant Fe species as basis species (to speed up calculation) 20210224",
        "Use loga_aq argument to control the activity of aqueous species in mosaic calculation 20220722",
        "c(NA, logm_aq) means to use:",
        "basis()'s value for logact of aqueous S species",
        "logm_aq for logact of aqueous Fe species",
        "Adjust labels",
        "Highlight Ccp and Bn in orange",
        "Thick line around Ccp field",
        "Add second Cu label",
        "Plot the Fe-system lines and names \"on top\" so they are not covered by fill colors",
        "Restore default OBIGT database",
        "Mixing 2",
        "Mosaic Stacking 3",
        "Fe-S-O-H diagram",
        "Order species by a function of composition to make colors",
        "Cu-Fe-S-O-H diagram based on reactions with the",
        "stable Fe-bearing minerals (mosaic stack)",
        "Mash the diagrams and adjust labels",
        "Function to calculate solubility of Cu for stable assemblages of Fe and Cu minerals",
        "(i.e. equilibrium is imposed with all of these minerals, not only Cu(s))",
        "DIAGRAM 1",
        "Calculate logK for CuCl2- dissociation at 125 °C",
        "Sverjensky (1987) used Helgeson (1969) value, which is ca. -5.2",
        "Calculate the difference in ΔG° corresponding to this logK difference",
        "We should use calories here because the database values are in calories 20220604",
        "Apply this difference to the CuCl2- entry in OBIGT",
        "Do the same thing for CuCl3-2",
        "DIAGRAM 2",
        "Set up system to dissolve S2(gas)",
        "Calculate concentration of SO4-2",
        "DIAGRAM 3",
        "Secondary Balancing",
        "PRIMARY balancing",
        "Only Fe-bearing minerals",
        "Only Cu-bearing minerals",
        "Only Fe- AND Cu-bearing minerals",
        "SECONDARY balancing",
        "Fe- or Cu-bearing minerals",
        "All minerals",
        "Other Possibilities",
        "Balancing on a Non-Metal",
        "Mosaic Combo",
        "A function to calculate Keff for any combination of T and pH",
        "Make T and pH the same length",
        "Calculate activity of H+",
        "Calculate logKs",
        "Calculate Ks",
        "Calculate Keff (Eq. 7)",
        "Calculate logKeff as a function of pH at 100 °C",
        "Calculate activity of acetamide for",
        "acetic acid + acetate = 0.01 m",
        "ammonia + ammonium = 0.001 m",
        "METHOD 2: Mosaic combo",
        "Define total activities",
        "This is 2 * 0.01 because acetic acid has 2 carbons",
        "Load all C-bearing species (including acetamide)",
        "Calculate distribution of C-bearing species accounting for ammonia/ammonium speciation",
        "Plot and label diagram",
        "Start with empty diagram",
        "Add pH = 6 line",
        "Add line for acetamide activity calculated with Keff",
        "Add lines from CHNOSZ calculations",
        "Check that we got equal values",
        "Document History",
        "References"
      ],
      "created": "2020-07-16 01:32:59",
      "modified": "2026-01-06 08:41:43",
      "commits": 71
    },
    {
      "source": "OBIGT.Rmd",
      "filename": "OBIGT.html",
      "title": "OBIGT thermodynamic database",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Aqueous Species <button id=\"B-aqueous-H2O\" onclick='ToggleDiv(\"aqueous-H2O\")'>H2O</button> <button id=\"B-aqueous-inorganic\" onclick='ToggleDiv(\"aqueous-inorganic\")'>Inorganic</button> <button id=\"B-aqueous-organic\" onclick='ToggleDiv(\"aqueous-organic\")'>Organic</button>",
        "Solids <button id=\"B-solid-inorganic\" onclick='ToggleDiv(\"solid-inorganic\")'>Inorganic</button> <button id=\"B-solid-organic\" onclick='ToggleDiv(\"solid-organic\")'>Organic</button> <button id=\"B-solid-Berman\" onclick='ToggleDiv(\"solid-Berman\")'>Berman</button>",
        "Gases <button id=\"B-gas-inorganic\" onclick='ToggleDiv(\"gas-inorganic\")'>Inorganic</button> <button id=\"B-gas-organic\" onclick='ToggleDiv(\"gas-organic\")'>Organic</button>    Liquids <button id=\"B-liquid-organic\" onclick='ToggleDiv(\"liquid-organic\")'>Organic</button>",
        "Optional Data <button id=\"B-optional-SUPCRT92\" onclick='ToggleDiv(\"optional-SUPCRT92\")'>SUPCRT92</button> <button id=\"B-optional-SLOP98\" onclick='ToggleDiv(\"optional-SLOP98\")'>SLOP98</button> <button id=\"B-optional-AD\" onclick='ToggleDiv(\"optional-AD\")'>AD</button> <button id=\"B-optional-DEW\" onclick='ToggleDiv(\"optional-DEW\")'>DEW</button> <button id=\"B-optional-Testing\" onclick='ToggleDiv(\"optional-Testing\")'>Testing</button>",
        "References"
      ],
      "created": "2020-07-04 04:53:42",
      "modified": "2025-10-17 00:48:15",
      "commits": 44
    },
    {
      "source": "eos-regress.Rmd",
      "filename": "eos-regress.html",
      "title": "Regressing thermodynamic data",
      "author": "Jeffrey M. Dick",
      "engine": "knitr::rmarkdown",
      "headings": [
        "A note on the equations",
        "A note on the algorithms",
        "An example for neutral species",
        "Setting the value of omega",
        "An example for charged species",
        "Doing it for volume",
        "Making a pseudospecies: r h4sio4",
        "References"
      ],
      "created": "2017-02-06 13:30:10",
      "modified": "2025-06-02 09:14:27",
      "commits": 41
    }
  ],
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