# CHNOSZ v1.3.2

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## Thermodynamic Calculations and Diagrams for Geochemistry

An integrated set of tools for thermodynamic calculations in aqueous geochemistry and geobiochemistry. Functions are provided for writing balanced reactions to form species from user-selected basis species and for calculating the standard molal properties of species and reactions, including the standard Gibbs energy and equilibrium constant. Calculations of the non-equilibrium chemical affinity and equilibrium chemical activity of species can be portrayed on diagrams as a function of temperature, pressure, or activity of basis species; in two dimensions, this gives a maximum affinity or predominance diagram. The diagrams have formatted chemical formulas and axis labels, and water stability limits can be added to Eh-pH, oxygen fugacity- temperature, and other diagrams with a redox variable. The package has been developed to handle common calculations in aqueous geochemistry, such as solubility due to complexation of metal ions, mineral buffers of redox or pH, and changing the basis species across a diagram ("mosaic diagrams"). CHNOSZ also has unique capabilities for comparing the compositional and thermodynamic properties of different proteins.

## Functions in CHNOSZ

 Name Description eos Equations of State eqdata Read data from an EQ6 output file nonideal Activity Coefficients of Aqueous Species objective Objective Functions util.blast Functions to Work with BLAST Output Files util.data Functions for Checking Thermodynamic Data util.matrix Functions for Various Matrix Operations util.misc Functions for Miscellaneous Tasks EOSregress Regress Equations-of-State Parameters for Aqueous Species IAPWS95 Properties of Water from IAPWS-95 palply Conditional Parallel Processing basis Define Basis Species protein Examples of Calculations for Proteins berman Thermodynamic Properties of Minerals NaCl Simple NaCl-Water Solution equilibrate Equilibrium Chemical Activities of Species examples Run Examples from the Documentation add.obigt Functions to Work with the Thermodynamic Database makeup Parse Chemical Formulas mosaic Chemical Affinities with Changing Basis Species util.expression Functions to Express Chemical Formulas and Properties util.fasta Functions for Reading FASTA Files and Downloading from UniProt util.seq Functions to Work with Sequence Data util.test Functions for Writing Tests water Properties of Water buffer Calculating Buffered Chemical Activities diagram Chemical Activity Diagrams wjd Gibbs Energy Minimization by Steepest Descent swap.basis Swap Basis Species taxonomy Extract Data from NCBI Taxonomy Files util.units Functions to Convert Units util.water Functions for Properties of Water and Steam add.protein Amino Acid Compositions of Proteins affinity Chemical Affinities of Formation Reactions CHNOSZ-package Thermodynamic Calculations and Diagrams for Geochemistry extdata Extra Data DEW Deep Earth Water (DEW) Model findit Gridded Search to Optimize Objective Functions info Search the Thermodynamic Database protein.info Summaries of Thermodynamic Properties of Proteins retrieve Retrieve Species by Element species Species of Interest ionize.aa Properties of Ionization of Proteins revisit Plots and Optima of Objective Functions subcrt Properties of Species and Reactions util.plot Functions to Create and Modify Plots solubility Equilibrium Chemical Activities of Species util.protein Functions for Proteins (Other Calculations) thermo Thermodynamic Database and System Settings yeast Composition, Localization, and Abundances of Proteins in Yeast util.array Functions to Work with Multidimensional Arrays util.formula Functions to Work with Chemical Formulas util.list Functions to Work with Lists No Results!

## Vignettes of CHNOSZ

 Name CHNOSZ.dia CHNOSZ.png anintro.Rmd elementa.csl eos-regress.Rmd equilibrium.Rnw equilibrium.lyx hotspring.Rnw hotspring.lyx mklinks.sh obigt.Rmd obigt.bib obigt.css rubisco.svg vig.bib vig.css No Results!