[CHNOSZ-commits] r641 - in pkg/CHNOSZ: . inst vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Feb 25 03:55:21 CET 2021 

Author: jedick
Date: 2021-02-25 03:55:21 +0100 (Thu, 25 Feb 2021)
New Revision: 641

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/vignettes/multi-metal.Rmd
   pkg/CHNOSZ/vignettes/vig.bib
Log:
multi-metal.Rmd: Add Keff calculation


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2021-02-25 01:13:32 UTC (rev 640)
+++ pkg/CHNOSZ/DESCRIPTION	2021-02-25 02:55:21 UTC (rev 641)
@@ -1,6 +1,6 @@
-Date: 2021-02-24
+Date: 2021-02-25
 Package: CHNOSZ
-Version: 1.4.0-10
+Version: 1.4.0-11
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2021-02-25 01:13:32 UTC (rev 640)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2021-02-25 02:55:21 UTC (rev 641)
@@ -10,29 +10,32 @@
 \newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
 \newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
 
-\section{Changes in CHNOSZ version 1.4.0-5 (2021-02-21)}{
+\section{Changes in CHNOSZ version 1.4.0-11 (2021-02-25)}{
 
-  \itemize{
+  \subsection{CHANGES}{
+    \itemize{
 
-    \item Remove limSolve from Suggests in DESCRIPTION.
+      \item Remove limSolve from Suggests in DESCRIPTION.
 
-    \item In the return value of \code{diagram()}, \code{predominant.values}
-    previously only contained affinities (extracted from the \code{values}
-    element of the \code{eout} argument). Now it has the values for the
-    predominant species extracted from the actual values used to make the plot
-    (the \code{plotvals} list in the output), i.e.  affinities divided by the
-    balancing coefficients if \code{eout} is the output of \code{affinity}, or
-    activities if \code{eout} is the output of \code{equilibrate}. Therefore it
-    can now be used to draw contours or a color image showing the activities of
-    the predominant species.
+      \item In the return value of \code{diagram()}, \code{predominant.values}
+      previously only contained affinities (extracted from the \code{values}
+      element of the \code{eout} argument). Now it has the values for the
+      predominant species extracted from the actual values used to make the plot
+      (the \code{plotvals} list in the output), i.e.  affinities divided by the
+      balancing coefficients if \code{eout} is the output of \code{affinity}, or
+      activities if \code{eout} is the output of \code{equilibrate}. Therefore it
+      can now be used to draw contours or a color image showing the activities of
+      the predominant species.
 
-    \item Use standard abbreviations for hematite (Hem) and magnetite (Mag) in
-    OBIGT/Berman_cr.csv.
+      \item Use standard abbreviations for hematite (Hem) and magnetite (Mag) in
+      OBIGT/Berman_cr.csv.
 
-    \item Revise multi-metal.Rmd: Improve mineral abbreviations and placement
-    of labels; use updated DFT energies from Materials Project; add Mosaic
-    Stacking 2 (minerals and aqueous species).
+      \item Revise multi-metal.Rmd: Improve mineral abbreviations and placement
+      of labels; use updated DFT energies from Materials Project; add Mosaic
+      Stacking 2 (minerals and aqueous species); add \emph{K}\s{eff} calculation
+      (\href{https://doi.org/10.1016/j.gca.2021.01.038}{Robinson et al., 2021}).
 
+    }
   }
 
 }

Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd	2021-02-25 01:13:32 UTC (rev 640)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd	2021-02-25 02:55:21 UTC (rev 641)
@@ -1024,26 +1024,85 @@
 Instead of adding minerals with different metals by stacking mosaic diagrams, it may be possible to include two different metals in the basis species and formed species.
 The `mosaic()` and `equilibrate()` functions can be combined to balance on two different elements.
 The example here is for N and C rather than metals.
+The "effective equilibrium constant" (*K*~eff~) method [@RBG_21] is used first to calculate the activity of acetamide for a total activities of neutral and ionized species, i.e. ∑(ammonia and ammonium) and ∑(acetic acid and acetate).
 
-First, the `mosaic()` command calculates equilibrium activities of NH~3~ and NH~4~^+^ for a given total activity of N in the basis species, and calculates the corresponding affinities of the formed species.
+In the mosaic combo method, the `mosaic()` command calculates equilibrium activities of NH~3~ and NH~4~^+^ for a given total activity of N in the basis species, and calculates the corresponding affinities of the formed species.
 Then, the `equilibrate()` command calculates equilibrium activities of the formed species for given total activity of C, and combines them with the activities of the changing basis species (NH~3~ and NH~4~^+^).
 
-```{r mosaic-combo, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "80%", fig.align = "center", pngquant = pngquant}
-loga_N <- -4
-loga_C <- -3
+The mosaic combo method (black line) produces results equivalent to those of the *K*~eff~ method (dashed blue line).
+
+<button id="B-mosaic-combo" onclick="ToggleDiv('mosaic-combo')">Show code</button>
+<div id="D-mosaic-combo" style="display: none">
+```{r mosaic-combo, eval = FALSE}
+## METHOD 1: Keff equation (Robinson et al., 2021)
+
+# A function to calculate Keff for any combination of T and pH
+Keff <- function(T = 25, pH = 7) {
+  # Make T and pH the same length
+  len <- max(length(T), length(pH))
+  T <- rep(T, length.out = len)
+  pH <- rep(pH, length.out = len)
+  # Calculate activity of H+
+  aH <- 10^(-pH)
+  # Calculate logKs
+  logK1 <- subcrt(c("acetic acid", "NH3", "acetamide", "H2O"), c(-1, -1, 1, 1), T = T)$out$logK
+  logK2 <- subcrt(c("acetic acid", "acetate", "H+"), c(-1, 1, 1), T = T)$out$logK
+  logK3 <- subcrt(c("NH3", "H+", "NH4+"), c(-1, -1, 1), T = T)$out$logK
+  # Calculate Ks
+  K1 <- 10^logK1
+  K2 <- 10^logK2
+  K3 <- 10^logK3
+  # Calculate Keff (Eq. 7)
+  Keff <- K1 * (1 + K2 / aH) ^ -1 * (1 + K3 * aH) ^ -1
+  Keff
+}
+
+# Calculate logKeff as a function of pH
+pH <- seq(0, 14, 0.1)
+logKeff <- log10(Keff(pH = pH))
+
+# Calculate activity of acetamide for
+# acetic acid + acetate = 0.001 m
+# ammonia + ammonium = 0.0001 m
+logAc <- log10(0.001)
+logAm <- log10(0.0001)
+logAcAm <- logKeff + logAc + logAm
+
+## METHOD 2: Mosaic combo
+
+# Define total activities
+a_N <- 0.0001
+# This is 2 * 0.001 because acetic acid has 2 carbons
+a_C <- 2 * 0.001
+loga_N <- log10(a_N)
+loga_C <- log10(a_C)
+# Setup basis species
 basis(c("CO2", "NH3", "O2", "H2O", "H+"))
 basis("NH3", loga_N)
+# Load all C-bearing species (including acetamide)
 species(c("acetamide", "acetic acid", "acetate"))
+# Calculate distribution of C-bearing species accounting for ammonia/ammonium speciation
 m <- mosaic(c("NH3", "NH4+"), pH = c(0, 14))
 e <- equilibrate(m, loga.balance = loga_C)
-diagram(e, ylim = c(-10, -2))
-tN <- paste("log(total N in basis species) =", loga_N)
-tC <- paste("log(total C in formed species) =", loga_C)
+
+# Plot and label diagram
+# Start with empty diagram
+diagram(e, ylim = c(-10, -2), lty = 0, names = FALSE)
+# Add line for acetamide activity calculated with Keff
+lines(pH, logAcAm, col = 4, lwd = 6, lty = 2)
+# Add lines from CHNOSZ calculations
+diagram(e, add = TRUE, dy = 0.1, dx = c(-0.2, 0.2, -1.7, 0, 0), lty = c(2, 3, 1, 2, 3), lwd = c(1, 1, 2, 1, 1))
+tN <- paste("Total N in basis species =", format(a_N, scientific = FALSE), "m")
+tC <- paste("Total C in formed species =", format(a_C, scientific = FALSE), "m")
 title(main = paste(tN, tC, sep = "\n"), font.main = 1)
 legend("topright", legend = lTP(25, 1), bty = "n")
 ```
+</div>
 
-The diagram shows the expected ionization of acetic acid and NH~3~ at different pHs.
+```{r mosaic-combo, echo = FALSE, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "80%", fig.align = "center", pngquant = pngquant}
+```
+
+The diagram shows the ionization of acetic acid and NH~3~ at different pHs.
 The predicted appearance of acetamide (CH~3~CONH~2~) is a consequence of the interaction between the N-bearing and C-bearing species, and is analogous to the formation of a bimetallic complex.
 
 *Thanks to Kirt Robinson for the feature request and test case used in this example.*
@@ -1051,6 +1110,6 @@
 ## Document History
 
 * 2020-07-15 First version.
-* 2021-02-21 Improve mineral abbreviations and placement of labels; use updated DFT energies from Materials Project; add Mosaic Stacking 2 (minerals and aqueous species).
+* 2021-02-25 Improve mineral abbreviations and placement of labels; use updated DFT energies from Materials Project; add Mosaic Stacking 2 (minerals and aqueous species); add *K*~eff~ calculation.
 
 ## References

Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib	2021-02-25 01:13:32 UTC (rev 640)
+++ pkg/CHNOSZ/vignettes/vig.bib	2021-02-25 02:55:21 UTC (rev 641)
@@ -924,3 +924,12 @@
   volume    = {97},
   doi       = {10.1016/j.commatsci.2014.10.037},
 }
+
+ at Article{RBG_21,
+  author    = {Kirtland J. Robinson and Christiana Bockisch and Ian R. Gould and Yiju Liao and Ziming Yang and Christopher R. Glein and Garrett D. Shaver and Hilairy E. Hartnett and Lynda B. Williams and Everett L. Shock},
+  journal   = {Geochimica et Cosmochimica Acta},
+  title     = {Quantifying the extent of amide and peptide bond synthesis across conditions relevant to geologic and planetary environments},
+  year      = {2021},
+  volume    = {in press},
+  doi       = {10.1016/j.gca.2021.01.038},
+}

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