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CHNOSZ (version 1.3.2)

Thermodynamic Calculations and Diagrams for Geochemistry

Description

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.

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Version

Install

install.packages('CHNOSZ')

Monthly Downloads

883

Version

1.3.2

License

GPL (>= 2)

Maintainer

Jeffrey Dick

Last Published

April 21st, 2019

Functions in CHNOSZ (1.3.2)

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