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logkcalc's Introduction

logKcalc

This R package calculates equilibrium constants for thermodynamic data files used in The Geochemist's Workbench®. It reads reactions from an existing GWB thermodynamic data file, calculates equilibrium constants (log K) for the reactions using the OBIGT database in CHNOSZ, and writes them to a new GWB thermodynamic data file.

Features

  • Change the temperature and pressure for log K calculations.
  • Update parameters for activity and osmotic coefficients (Debye-Hückel, H2O, CO2) for specified T and P.
  • Add new species to the output file.
  • List data references in the output file (requires CHNOSZ version > 1.3.6).
  • Make plots comparing log K values from two data files.
  • Update OBIGT using thermodynamic parameters (ΔG°, S° and Cp°) fitted to log K values from a GWB file.
    • Enables addition of species from a GWB file to calculations and diagrams in CHNOSZ.

Installation

install.packages("remotes")
remotes::install_github("jedick/logKcalc", build_vignettes = TRUE, dependencies = TRUE)

Documentation

See the vignettes for detailed usage examples.

logkcalc's People

Contributors

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logkcalc's Issues

A trouble encountered during the installation of logKcal

Hello, I am a beginner of R language user, and I have some trouble in installing the "logKcal" package through the Rstudio IDE.

I do not have any trouble in installing the package of "CHNOSZ". However, I find I cannot successfully install the ''logKcal''

The error prompt is like the below:
Error: Failed to install 'logKcalc' from GitHub:
System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
E> Quitting from lines 137-137 (vig5.Rmd)
E> Error: processing vignette 'vig5.Rmd' failed with diagnostics:
E> species not available: As(OH)3()
E> --- failed re-building 'vig5.Rmd'
E>
E> SUMMARY: processing the following files failed:
E> 'vig1.Rmd' 'vig2.Rmd' 'vig5.Rmd'
E>
E> Error: Vignette re-building failed.
E> Execution halted

If anybody can help me solve this problem, I will be greatly appreciated.

Thanks in advance!

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