[CHNOSZ-commits] r856 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT inst/extdata/adds inst/extdata/thermo vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 24 14:16:35 CET 2024
Author: jedick
Date: 2024-12-24 14:16:34 +0100 (Tue, 24 Dec 2024)
New Revision: 856
Added:
pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/util.data.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/vignettes/OBIGT.Rmd
Log:
Move Knight et al. (2024) to optional data
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2024-12-23 10:30:11 UTC (rev 855)
+++ pkg/CHNOSZ/DESCRIPTION 2024-12-24 13:16:34 UTC (rev 856)
@@ -1,6 +1,6 @@
-Date: 2024-12-23
+Date: 2024-12-24
Package: CHNOSZ
-Version: 2.1.0-28
+Version: 2.1.0-29
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/R/util.data.R
===================================================================
--- pkg/CHNOSZ/R/util.data.R 2024-12-23 10:30:11 UTC (rev 855)
+++ pkg/CHNOSZ/R/util.data.R 2024-12-24 13:16:34 UTC (rev 856)
@@ -272,6 +272,7 @@
else if(what == "AD") tdata <- read.csv(system.file("extdata/OBIGT/AD.csv", package = "CHNOSZ"), as.is = TRUE)
else if(what == "GEMSFIT") tdata <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package = "CHNOSZ"), as.is = TRUE)
else if(what == "IGEM24") tdata <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE)
+ else if(what == "KBJ24") tdata <- read.csv(system.file("extdata/OBIGT/KBJ24.csv", package = "CHNOSZ"), as.is = TRUE)
ntot <- nrow(tdata)
# Where to keep the results
DCp <- DV <- DG <- rep(NA, ntot)
@@ -310,6 +311,7 @@
out <- rbind(out, checkfun("AS04"))
out <- rbind(out, checkfun("GEMSFIT"))
out <- rbind(out, checkfun("IGEM24"))
+ out <- rbind(out, checkfun("KBJ24"))
# Set differences within a tolerance to NA
out$DCp[abs(out$DCp) < 1] <- NA
out$DV[abs(out$DV) < 1] <- NA
@@ -394,8 +396,10 @@
GEMSFIT <- cbind(source = "GEMSFIT", dat)
dat <- read.csv(system.file("extdata/OBIGT/IGEM24.csv", package = "CHNOSZ"), as.is = TRUE)
IGEM24 <- cbind(source = "IGEM24", dat)
+ dat <- read.csv(system.file("extdata/OBIGT/KBJ24.csv", package = "CHNOSZ"), as.is = TRUE)
+ KBJ24 <- cbind(source = "KBJ24", dat)
# Put it all together
- out <- rbind(OBIGT, SUPCRT92, SLOP98, AS04, AD, DEW, GEMSFIT, IGEM24)
+ out <- rbind(OBIGT, SUPCRT92, SLOP98, AS04, AD, DEW, GEMSFIT, IGEM24, KBJ24)
# Quote columns 2 (name) and 3 (abbrv) because they have commas for some entries
if(!is.null(file)) write.csv(out, file, row.names = FALSE, quote = c(2, 3))
else(return(out))
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2024-12-23 10:30:11 UTC (rev 855)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-24 13:16:34 UTC (rev 856)
@@ -15,10 +15,55 @@
\newcommand{\Cp}{\ifelse{latex}{\eqn{C_P}}{\ifelse{html}{\out{<I>C<sub>P</sub></I>}}{Cp}}}
\newcommand{\DG0}{\ifelse{latex}{\eqn{{\Delta}G^{\circ}}}{\ifelse{html}{\out{Δ<I>G</I>°}}{ΔG°}}}
-\section{Changes in CHNOSZ version 2.1.0-28 (2024-12-23)}{
+\section{Changes in CHNOSZ version 2.1.0-29 (2024-12-24)}{
+ \subsection{OBIGT DEFAULT DATA}{
\itemize{
+ \item Add aqueous uranyl complexes from
+ \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}
+ and related U-bearing minerals from
+ \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}.
+
+ \item Move americium complexes from \file{slop98.dat} back to
+ \file{inorganic_aq.csv} (entropy of the element Am has been available for
+ checking GHS self-consistency since version 1.4.0).
+
+ \item Add alkylamines, benzylamines, and aminiums from
+ \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}.
+
+ \item \samp{OBIGT/inorganic_cr.csv}: Add cerianite (CeO\s{2}) and
+ chromite (FeCr\s{2}O\s{4}) from
+ \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}.
+
+ \item Restore steam (H\s{2}O,g) in \file{inorganic_gas.csv}.
+
+ \item Fix sign of \emph{c} parameter for nesquehonite. Thanks to
+ James Leong and Grayson Boyer.
+
+ }
+ }
+
+ \subsection{OBIGT OPTIONAL DATA}{
+ \itemize{
+
+ \item Except for HUO\s{4}\S{-}, aqueous uranium species from
+ \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)}
+ have been moved to \file{SLOP98.csv}.
+
+ \item \file{IGEM24.csv}: updated data for Au and Cu complexes and
+ SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS.
+
+ \item \file{KBJ24.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
+ \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
+ (2024)}.
+
+ }
+ }
+
+ \subsection{NEW FEATURES}{
+ \itemize{
+
\item Move \code{read.fasta()}, \code{count.aa()}, and \code{aasum()} to
canprot package with different names.
@@ -34,29 +79,9 @@
and \emph{Q} that are consistent with either SUPCRT92 or DEW, depending
on the \code{model} defined in OBIGT (HKF or DEW, respectively).
- \item Add aqueous uranyl complexes from
- \href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}
- and related U-bearing minerals from
- \href{https://doi.org/10.1787/bf86a907-en}{Grenthe et al. (2020)}.
-
- \item Except for HUO\s{4}\S{-}, aqueous uranium species from
- \href{https://doi.org/10.1016/S0016-7037(97)00240-8}{Shock et al. (1997)}
- have been moved to \file{SLOP98.csv}.
-
\item Remove \code{ispecies} from output of \code{check.OBIGT()} to avoid
superfluous diffs.
- \item Move americium complexes from \file{slop98.dat} back to
- \file{inorganic_aq.csv} (entropy of the element Am has been available for
- checking GHS self-consistency since version 1.4.0).
-
- \item Add alkylamines, benzylamines, and aminiums from
- \href{https://doi.org/10.1016/j.gca.2024.03.013}{Robinson et al. (2024)}.
-
- \item \samp{OBIGT/inorganic_cr.csv}: Add cerianite (CeO\s{2}) and
- chromite (FeCr\s{2}O\s{4}) from
- \href{https://doi.org/10.3133/b2131}{Robie and Hemingway (1995)}.
-
\item Add \file{demo/total_S.R} (total activity of S--pH diagram for
Fe-S-O-C minerals).
@@ -63,11 +88,6 @@
\item Restore \code{lines} to the output of \code{diagram()} for the x
and y values of predominance field boundaries.
- \item OBIGT: Restore steam (H\s{2}O,g) in \file{inorganic_gas.csv}.
-
- \item OBIGT: Fix sign of \emph{c} parameter for nesquehonite. Thanks to
- James Leong and Grayson Boyer.
-
\item Add \file{demo/uranyl.R}, total (carbonate|sulfate)-pH diagrams
for uranyl species, after
\href{https://doi.org/10.1016/j.gca.2024.04.023}{Migdisov et al. (2024)}.
@@ -78,20 +98,13 @@
\item Rename \file{demo/total_S.R} to \file{demo/sum_S.R}, change axes,
and add solubility contours for Fe and Au.
- \item Add \file{OBIGT/IGEM24.csv} with updated data for Au and Cu
- complexes and SO\s{4}\S{-2}-bearing species from
- researchers at IGEM RAS.
-
\item For better readability, formulas of species are no longer
subscripted by \code{axis.label()} (via \code{expr.species()}). An
example of the new formatting is log \emph{f}O\s{2}). Similar formatting
for other expressions has been used in the vignettes.
- \item OBIGT: Add Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
- \href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
- (2024)}.
-
}
+ }
}
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2024-12-23 10:30:11 UTC (rev 855)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv 2024-12-24 13:16:34 UTC (rev 856)
@@ -8,6 +8,7 @@
anorthite,An,Al2CaSi2O8,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
anthophyllite,Ath,Mg7Si8O24H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
antigorite,Atg,Mg48Si34O99H62O48,cr,Ber88,BDat17.1,2017-10-09,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+brucite,Brc,MgO2H2,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Ca-Al-pyroxene,CTs,CaAl2SiO6,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
calcite,Cal,CaCO3,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
chrysotile,Ctl,Mg3Si2O9H4,cr,Ber88,NA,2017-10-01,Berman,J,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Added: pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/KBJ24.csv 2024-12-24 13:16:34 UTC (rev 856)
@@ -0,0 +1,8 @@
+name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000
+bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000
+"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000
+"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000
+"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000
+"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000
+"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-12-23 10:30:11 UTC (rev 855)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_cr.csv 2024-12-24 13:16:34 UTC (rev 856)
@@ -160,10 +160,3 @@
Na2U2O7,Na2U2O7,Na2U2O7,cr,NEA20,NA,2023-08-07,CGL,J,-3011454,-3203800,275.9,227.3,0,262.83,0.014653,-3549000,0,0,0,0,1273
chromite,Chr,FeCr2O4,cr,RH95,NA,2024-05-23,CGL,J,-1344500,-1445500,146,133.58,44.01,301.8,-0.04157,487700,-2803,1.147E-05,0,0,-1800
cerianite,Cei,CeO2,cr,RH95,NA,2024-05-23,CGL,J,-1024600,-1088700,62.3,61.63,23.85,80.29,0.005699,-729400,-209.9,0,0,0,-1800
-brucite,NA,Mg(OH)2,cr,KBJ24,RH95.8,2024-12-23,CGL,J,-831798,-922826,63.199,74.99,24.63,80.764,0.00157,-550000,0,-5.77E-07,0,0,1000
-bischofite,NA,MgCl2*6H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2115074,-2499458,366.083,389.74,NA,300,0.387,-550000,0,-0.000224,0,0,1000
-"magnesium chloride tetrahydrate",NA,MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-1624923,-1900649,263.982,255.44,NA,255.44,0,0,0,-1.04E-10,0,0,1000
-"3-1-8 phase",NA,Mg2(OH)3Cl*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2554730,-2942309,313.7,286.07,NA,204.93,0.286,-272000,0,-1.22E-05,0,0,1000
-"2-1-2 phase",NA,Mg2(OH)4MgCl2*2H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-2815800,-3158670,309.17,293.73,NA,243.72,0.275,-2300000,0,-6.85E-05,0,0,1000
-"2-1-4 phase",NA,Mg2(OH)4MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-3306055,-3762785,393.89,362.08,NA,363.70,2.62E-08,0,0,-6.76E-05,0,0,1000
-"9-1-4 phase",NA,Mg9(OH)18MgCl2*4H2O,cr,KBJ24,NA,2024-12-23,CGL,J,-9136206,-10228288,842.43,885.06,NA,766.4,0.834,-10700000,0,-0.000108,0,0,1000
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-23 10:30:11 UTC (rev 855)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2024-12-24 13:16:34 UTC (rev 856)
@@ -310,7 +310,6 @@
"OBIGT","ferberite","cr","J",1.21,,
"OBIGT","willemite","cr","J",-1.47,,
"OBIGT","rutherfordine","cr","J",-14.37,,
-"OBIGT","2-1-4 phase","cr","J",-4.39,,
"OBIGT","octadecane","cr","cal",-2.63,,
"OBIGT","nonadecane","cr","cal",-13.32,,
"OBIGT","eicosane","cr","cal",-2.79,,
@@ -400,3 +399,4 @@
"SUPCRT92","greenalite","cr","cal",,,142507
"SUPCRT92","grunerite","cr","cal",9.72,,
"SUPCRT92","halloysite","cr","cal",-1.6,,
+"KBJ24","2-1-4 phase","cr","J",-4.39,,
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-23 10:30:11 UTC (rev 855)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2024-12-24 13:16:34 UTC (rev 856)
@@ -206,7 +206,7 @@
### Aqueous Species <button id="B-aqueous-H2O" onclick='ToggleDiv("aqueous-H2O")'>H2O</button> <button id="B-aqueous-inorganic" onclick='ToggleDiv("aqueous-inorganic")'>Inorganic</button> <button id="B-aqueous-organic" onclick='ToggleDiv("aqueous-organic")'>Organic</button>
### Solids <button id="B-solid-inorganic" onclick='ToggleDiv("solid-inorganic")'>Inorganic</button> <button id="B-solid-organic" onclick='ToggleDiv("solid-organic")'>Organic</button> <button id="B-solid-Berman" onclick='ToggleDiv("solid-Berman")'>Berman</button>
### Gases <button id="B-gas-inorganic" onclick='ToggleDiv("gas-inorganic")'>Inorganic</button> <button id="B-gas-organic" onclick='ToggleDiv("gas-organic")'>Organic</button> Liquids <button id="B-liquid-organic" onclick='ToggleDiv("liquid-organic")'>Organic</button>
-### Optional Data <button id="B-optional-SUPCRT92" onclick='ToggleDiv("optional-SUPCRT92")'>SUPCRT92</button> <button id="B-optional-SLOP98" onclick='ToggleDiv("optional-SLOP98")'>SLOP98</button> <button id="B-optional-AD" onclick='ToggleDiv("optional-AD")'>AD</button> <button id="B-optional-AS04" onclick='ToggleDiv("optional-AS04")'>AS04</button> <button id="B-optional-DEW" onclick='ToggleDiv("optional-DEW")'>DEW</button> <button id="B-optional-GEMSFIT" onclick='ToggleDiv("optional-GEMSFIT")'>GEMSFIT</button> <button id="B-optional-IGEM24" onclick='ToggleDiv("optional-IGEM24")'>IGEM24</button>
+### Optional Data <button id="B-optional-SUPCRT92" onclick='ToggleDiv("optional-SUPCRT92")'>SUPCRT92</button> <button id="B-optional-SLOP98" onclick='ToggleDiv("optional-SLOP98")'>SLOP98</button> <button id="B-optional-AD" onclick='ToggleDiv("optional-AD")'>AD</button> <button id="B-optional-AS04" onclick='ToggleDiv("optional-AS04")'>AS04</button> <button id="B-optional-DEW" onclick='ToggleDiv("optional-DEW")'>DEW</button> <button id="B-optional-GEMSFIT" onclick='ToggleDiv("optional-GEMSFIT")'>GEMSFIT</button> <button id="B-optional-IGEM24" onclick='ToggleDiv("optional-IGEM24")'>IGEM24</button> <button id="B-optional-KBJ24" onclick='ToggleDiv("optional-KBJ24")'>KBJ24</button>
<!-- Normal or "all open" footer message -->
@@ -397,6 +397,15 @@
```
</div>
+<div id="D-optional-KBJ24" style="display: none">
+## <a id="optional-KBJ24" class="anchor"></a> `r setfile("KBJ24.csv")`
+Model for the Mg(OH)<sub>2</sub>-MgCl<sub>2</sub>-H<sub>2</sub>O system from 25 to 150 °C.
+Use `add.OBIGT("KBJ24")` to load the data.
+
+```{r optreflist, results="asis", echo=FALSE}
+```
+</div>
+
<hr>
<b>Total count of species</b>: References were found for `r length(used)` of `r nrow(thermo()$OBIGT)` species in the default OBIGT database and `r length(optused)` optional species.
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