In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

library(knitr)
## Use pngquant to reduce size of PNG images
knit_hooks$set(pngquant = hook_pngquant)
pngquant <- "--speed=1 --quality=0-25"
# In case pngquant isn't available
if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL 

# Thermodynamic properties
DG0f <- "&Delta;<i>G</i>&deg;<sub><i>f</i></sub>"
S0 <- "<i>S</i>&deg;"
Cp <- "<i>C<sub>p</sub></i>"
logK <- "log&thinsp;<i>K</i>"
logfO2 <- "log<i>f</i><sub>O<sub>2</sub></sub>"

This vignette runs the code to make selected plots from the following paper:

von der Heyden BP, Dick J, Rosenfels RC, Carlton L, Lilova K, Navrotsky A, Subramani T, Woodfield BF, Gibson A 2024. Growth and stability of stratiform carrollite (CuCo~2~S~4~) in the Tenke-Fungurume ore district, Central African Copperbelt. The Canadian Journal of Mineralogy and Petrology 62(1): 77--93. doi: 10.3389/feart.2019.00180

This vignette was compiled on r Sys.Date() with JMDplots r packageDescription("JMDplots")$Version and CHNOSZ r packageDescription("CHNOSZ")$Version.

library(JMDplots)
# Set plot resolution
res <- if(nzchar(Sys.getenv("BUILD_LARGE_VIGNETTES"))) 400 else 75

Check thermodynamic parameters for carrollite

This compares the thermodynamic parameters for carrollite in the OBIGT database with values calculated on-the-fly. The latter values include computed parameters for the high-temperature polymorph and heat capacity coefficients for both polymorphs. After the test, we reset the OBIGT database so the testing data don't get in the way of the following calculations.

# Calculate parameters
calc <- calc_carrollite()
# Get parameters stored in OBIGT
ref <- info(info("carrollite", c("cr", "cr2")))
# Columns of OBIGT with parameters to check
ichk <- 10:22
stopifnot(all.equal(calc$cr[, ichk], ref[1, ichk], check.attributes = FALSE, tolerance = 1e-4))
stopifnot(all.equal(calc$cr2[, ichk], ref[2, ichk], check.attributes = FALSE, tolerance = 1e-4))
reset()

Add thermodynamic parameters for aqueous Co complexes

This uses CHNOSZ::logB.to.OBIGT() to fit formation constants for aqueous Co complexes [@MZW11] to an equation with two adjustable parameters (r DG0f and r S0) that are then added to OBIGT.

complexes <- add_Co_aqueous()

The fitted parameters are listed below for comparison with Table 1 in the paper.

Co <- info(info(c("CoCl+", "CoCl2", "CoCl3-", "CoCl4-2")))
Co$G <- round(Co$G)
Co$H <- round(Co$H)
Co$S <- round(Co$S, 3)
rownames(Co) <- Co$name
kable(Co[, c("G", "H", "S")])

r logfO2-pH diagram with carrollite (Figure 5)

carrollite_5(res)

Comparison of Cu-Co and Fe-Cu diagrams (Figure 8)

carrollite_8(res)

Experimental and fitted r Cp for carrollite (Figure S3)

carrollite_S3()

Experimental and fitted formation constants for Cl^-^ complexes (Figure S4)

carrollite_S4(complexes)

r logK of reactions showing temperatures of linnaeite in and carrollite out (Figure S5)

carrollite_S5()

Compare mosaic stack (with carrollite) to CHNOSZ::solubility() calculation for Co or Cu without carrollite (Figure S6)

carrollite_S6(res)

References

jedick/JMDplots documentation built on April 12, 2025, 1:35 p.m.