Python wrapper for the R package CHNOSZ by Dr. Jeffrey Dick
Project description
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 H2 (aq) + 0.5 O2 (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 }
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