Thermodynamic Calculations and Diagrams for Geochemistry
Functions to Work with the Thermodynamic Database
Amino Acid Compositions of Proteins
Chemical Affinities of Formation Reactions
Define Basis Species
Thermodynamic Properties of Minerals
Calculating Buffered Chemical Activities
Thermodynamic Calculations and Diagrams for Geochemistry
Deep Earth Water (DEW) Model
Chemical Activity Diagrams
Regress Equations-of-State Parameters for Aqueous Species
Equilibrium Chemical Activities of Species
Run Examples from the Documentation
Extra Data
Properties of Water from IAPWS-95
Search the Thermodynamic Database
Properties of Ionization of Proteins
Fit Thermodynamic Parameters to Formation Constants ( )
Parse Chemical Formulas
Combine Diagrams for Multi-Metal Systems
Chemical Affinities with Changing Basis Species
Simple NaCl-Water Solution
Activity Coefficients of Aqueous Species
Conditional Parallel Processing
Summaries of Thermodynamic Properties of Proteins
Average Ranks of Chemical Affinities
Retrieve Species by Element
Equilibrium Chemical Activities of Species
Species of Interest
Stacked mosaic diagram
Properties of Species and Reactions
Swap Basis Species
Extract Data from NCBI Taxonomy Files
Thermodynamic Database and System Settings
Functions to Work with Multidimensional Arrays
Functions for Checking Thermodynamic Data
Functions to Express Chemical Formulas and Properties
Functions for Reading FASTA Files and Downloading from UniProt
Functions to Work with Chemical Formulas
Functions to Make Legend Text
Functions to Work with Lists
Functions for Miscellaneous Tasks
Functions to Create and Modify Plots
Functions for Proteins (Other Calculations)
Functions to Work with Sequence Data
Functions to Convert Units
Functions for Properties of Water and Steam
Properties of Water
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 implements a group additivity algorithm for the standard thermodynamic properties of proteins.