pyCHNOSZ 0.0.2

Python wrapper for the R package CHNOSZ by Dr. Jeffrey Dick

pyCHNOSZ

Author: Dr. Grayson Boyer, GEOPIG Lab, Arizona State University

This is a python wrapper for certain functions in the R package CHNOSZ by Dr. Jeffrey Dick.

Features

Currently, the following CHNOSZ functions are supported in pyCHNOSZ:

• info - Search for chemical species by name or formula and retrieve their thermodynamic parameters.
• subcrt - Calculate standard state partial molal thermodynamic properties of reactions at elevated temperatures and pressures.

Requirements

This package must be installed into an environment that has an R installation. See these instructions for installing R with Anaconda. Additionally, the CHNOSZ package for R must be installed (see instructions below).

Installation

Installing CHNOSZ

Open an R session. Install the CHNOSZ package with:

install.packages("CHNOSZ")

Once CHNOSZ is installed you may quit the R session.

Installing pyCHNOSZ

Install pyCHNOSZ using pip:

$ pip install pyCHNOSZ

Usage

Search for chemical species

The info function can be used to look up chemical species by name or formula. If names or formulas are provided, database index integers are returned. A list of integers will look up chemical species by index and return a table of thermodynamic properties. See the info function's original documentation to learn more about what this function can do. A few examples are shown below.

Look up the database index value of Fe+2:

info("Fe+2")

Look up multiple chemical species:

info(["HCO3-", "CH4"])

Define chemical states:

info(["HCO3-", "CH4"], state=["aq", "gas"])

Search species by index values to look up their thermodynamic parameters.

info([13, 872])

Nest info functions to look up thermodynamic properties directly from names or formulas:

info(info("Fe+2"))

Look up and add a protein to the database:

info("LYSC_CHICK")

Calculate thermodynamic properties of reactions

See the original documentation for subcrt. Useage in pyCHNOSZ is the same, except python lists are used in place of R's vectors. The function produces a dictionary of results stored in pandas dataframes. An example is shown below for the reaction H_{2 (aq)} + 0.5 O_{2 (gas)} = H₂O_(liq) at 30 and 50 degrees C and 100 bars pressure:

subcrt(species=["H2", "O2", "H2O"], coeff=[-1.0, -0.5, 1.0],
       state=["aq", "gas", "liq"], T=[30, 50], P=100)

Output is a python dictionary of dataframes:

subcrt: 3 species at 2 values of T (ºC) and P (bar) (wet) [energy units: cal]

{'reaction':       coeff    name formula state  ispecies
 62     -1.0      H2      H2    aq      62.0
 2612   -0.5  oxygen      O2   gas    2612.0
 1       1.0   water     H2O   liq       1.0,
 'out':       T    P       rho       logK             G             H         S  \
 1  30.0  100  1.000017  43.855086 -60832.380282 -67420.887872 -21.89070   
 2  50.0  100  0.992305  40.834419 -60379.262657 -67882.530994 -23.36663   

           V         Cp  
 1 -7.494052 -24.126268  
 2 -8.259704 -20.941879  }