[CHNOSZ-commits] r721 - 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
Mon Apr 11 04:27:41 CEST 2022
Author: jedick
Date: 2022-04-11 04:27:40 +0200 (Mon, 11 Apr 2022)
New Revision: 721
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/NAMESPACE
pkg/CHNOSZ/R/thermo.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv
pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
pkg/CHNOSZ/inst/extdata/OBIGT/organic_gas.csv
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/OBIGT.bib
pkg/CHNOSZ/vignettes/customizing.Rmd
Log:
OBIGT: Move aqueous CH4 back to organic_aq.csv
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/DESCRIPTION 2022-04-11 02:27:40 UTC (rev 721)
@@ -1,6 +1,6 @@
-Date: 2022-04-09
+Date: 2022-04-11
Package: CHNOSZ
-Version: 1.9.9-13
+Version: 1.9.9-14
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/NAMESPACE
===================================================================
--- pkg/CHNOSZ/NAMESPACE 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/NAMESPACE 2022-04-11 02:27:40 UTC (rev 721)
@@ -72,7 +72,7 @@
"plot.new", "plot.window", "points", "rect", "text", "title")
importFrom("stats", "D", "as.formula", "cor", "lm", "loess.smooth",
"na.omit", "predict.lm", "qqline", "qqnorm", "sd", "splinefun",
- "uniroot", "median", "predict", "smooth.spline", "optimize")
+ "uniroot", "median", "predict", "smooth.spline", "optimize", "formula")
importFrom("utils", "browseURL", "capture.output", "combn", "demo",
"example", "head", "installed.packages", "read.csv", "tail",
"write.csv", "write.table", "read.table", "packageDescription")
Modified: pkg/CHNOSZ/R/thermo.R
===================================================================
--- pkg/CHNOSZ/R/thermo.R 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/R/thermo.R 2022-04-11 02:27:40 UTC (rev 721)
@@ -49,57 +49,57 @@
OBIGT()
}
-# load default thermodynamic data (OBIGT) in thermo
+# Load default thermodynamic data (OBIGT) in thermo
OBIGT <- function(no.organics = FALSE) {
- # we only work if thermo is already in the CHNOSZ environment
+ # We only work if thermo is already in the CHNOSZ environment
if(!"thermo" %in% ls(CHNOSZ)) stop("The CHNOSZ environment doesn't have a \"thermo\" object. Try running reset()")
- # create OBIGT data frame
- if(no.organics) {
- sources_aq <- paste0(c("H2O", "inorganic"), "_aq")
- sources_cr <- paste0(c("inorganic", "Berman"), "_cr")
- sources_gas <- paste0(c("inorganic"), "_gas")
- sources <- c(sources_aq, sources_cr, sources_gas)
- } else {
- sources_aq <- paste0(c("H2O", "inorganic", "organic"), "_aq")
- sources_cr <- paste0(c("inorganic", "organic", "Berman"), "_cr")
- sources_liq <- paste0(c("organic"), "_liq")
- sources_gas <- paste0(c("inorganic", "organic"), "_gas")
- sources <- c(sources_aq, sources_cr, sources_gas, sources_liq)
- }
- OBIGTdir <- system.file("extdata/OBIGT/", package="CHNOSZ")
- # need explicit "/" for Windows
- sourcefiles <- paste0(OBIGTdir, "/", sources, ".csv")
- datalist <- lapply(sourcefiles, read.csv, as.is=TRUE)
+ # Identify OBIGT data files
+ sources_aq <- paste0(c("H2O", "inorganic", "organic"), "_aq")
+ sources_cr <- paste0(c("inorganic", "organic", "Berman"), "_cr")
+ sources_liq <- paste0(c("organic"), "_liq")
+ sources_gas <- paste0(c("inorganic", "organic"), "_gas")
+ sources <- c(sources_aq, sources_cr, sources_gas, sources_liq)
+ OBIGTdir <- system.file("extdata/OBIGT/", package = "CHNOSZ")
+ # Read data from each file
+ datalist <- lapply(sources, function(source) {
+ # Need explicit "/" for Windows
+ file <- paste0(OBIGTdir, "/", source, ".csv")
+ dat <- read.csv(file, as.is = TRUE)
+ # Include CH4 with no.organics = TRUE 20220411
+ if(no.organics & grepl("^organic", source)) dat <- subset(dat, formula == "CH4")
+ dat
+ })
+ # Create OBIGT data frame
OBIGT <- do.call(rbind, datalist)
- # also read references file
- refs <- read.csv(file.path(OBIGTdir, "refs.csv"), as.is=TRUE)
- # get thermo from CHNOSZ environment
+ # Also read references file
+ refs <- read.csv(file.path(OBIGTdir, "refs.csv"), as.is = TRUE)
+ # Get thermo from CHNOSZ environment
thermo <- get("thermo", CHNOSZ)
- # set OBIGT and refs
+ # Set OBIGT and refs
thermo$OBIGT <- OBIGT
thermo$refs <- refs
- # place modified thermo in CHNOSZ environment
+ # Place modified thermo in CHNOSZ environment
assign("thermo", thermo, CHNOSZ)
- # give a summary of some of the data
+ # Give a summary of some of the data
message(paste("OBIGT: loading", ifelse(no.organics, "inorganic", "default"), "database with",
- nrow(thermo$OBIGT[thermo$OBIGT$state=="aq",]),
+ nrow(thermo$OBIGT[thermo$OBIGT$state == "aq",]),
"aqueous,", nrow(thermo$OBIGT), "total species"))
- # warn if there are duplicated species
+ # Warn if there are duplicated species
idup <- duplicated(paste(thermo$OBIGT$name, thermo$OBIGT$state))
if(any(idup)) warning("OBIGT: duplicated species: ",
- paste(thermo$OBIGT$name[idup], "(", thermo$OBIGT$state[idup], ")", sep="", collapse=" "))
+ paste(thermo$OBIGT$name[idup], "(", thermo$OBIGT$state[idup], ")", sep = "", collapse = " "))
}
-# a function to access or modify the thermo object 20190214
+# A function to access or modify the thermo object 20190214
thermo <- function(...) {
args <- list(...)
- # get the object
+ # Get the object
thermo <- get("thermo", CHNOSZ)
if(length(args) > 0) {
- # assign into the object
+ # Assign into the object
slots <- names(args)
for(i in 1:length(slots)) {
- # parse the name of the slot
+ # Parse the name of the slot
names <- strsplit(slots[i], "$", fixed=TRUE)[[1]]
if(length(names) == 1) thermo[[names]] <- args[[i]]
if(length(names) == 2) thermo[[names[1]]][[names[2]]] <- args[[i]]
@@ -106,7 +106,7 @@
}
assign("thermo", thermo, CHNOSZ)
} else {
- # return the object
+ # Return the object
thermo
}
}
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-04-11 02:27:40 UTC (rev 721)
@@ -10,7 +10,7 @@
\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 1.9.9-12 (2022-04-07)}{
+\section{Changes in CHNOSZ version 1.9.9-14 (2022-04-11)}{
\subsection{MAJOR CHANGE}{
\itemize{
@@ -31,20 +31,14 @@
\subsection{OBIGT DATABASE}{
\itemize{
- \item Add the following \emph{Disclaimer} to the Aqueous Inorganic
- section of \strong{OBIGT.Rmd}: To make the database easier to maintain,
- inorganic and organic species have been placed into separate data files,
- but some ambiguities surround the usage of these \emph{-ic} words in
- different contexts. In particular, while CH\s{4} (methane) is classified
- in chemistry as an organic compound, in nature it can be derived from
- living organisms or formed abiotically
- (\href{https://doi.org/10.1002/rog.20011}{Etiope and Sherwood Lollar,
- 2013}) – that is, through inorganic processes. For practical reasons,
- CH\s{4} is placed in the \dQuote{inorganic} data files in OBIGT simply so
- that the database can be pruned of organic compounds \emph{except}
- CH\s{4} by running \code{OBIGT(no.organics = TRUE)}. The ability to
- remove hundreds of more complex organic compounds while keeping CH\s{4}
- is useful for some models of inorganic reactions in hydrothermal systems.
+ \item Move aqueous CH\s{4} back to \file{organic_aq.csv}. Thanks to
+ Irucka Embry for flagging this. Also move gaseous CH\s{4} from
+ \file{inorganic_gas.csv} to \file{organic_gas.csv}.
+
+ \item Modify \code{OBIGT(no.organics = TRUE)} to prune the database of
+ organic compounds \emph{except} CH\s{4}. The ability to remove hundreds
+ of more complex organic compounds while keeping CH\s{4} is useful for
+ some models of inorganic reactions in hydrothermal systems.
\item Merge \file{biotic_aq.csv} into \file{organic_aq.csv}.
@@ -58,8 +52,8 @@
(\samp{G}, \samp{S}, and \samp{Cp} at 25 \degC) to formation constants of
aqueous species as a function of temperature.
- \item Add \code{zap} argument to \code{mod.OBIGT()} to clear parameters
- of preexisting species.
+ \item Add a \strong{zap} argument to \code{mod.OBIGT()} to clear
+ parameters of preexisting species.
\item Add vignette \strong{customizing.Rmd} with description of database
format, data-entry conventions, and examples of customizing the
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv 2022-04-11 02:27:40 UTC (rev 721)
@@ -702,7 +702,6 @@
RhO+,RhO+,RhO+,aq,SS98a,NA,1994-07-25,cal,3140,-10010,-18.7,-39.5,1.9,2.3067,-2.1515,6.6002,-2.69,-9.3049,-11.0806,0.8334,1
Ar,Ar,Ar,aq,PS01.1,NA,2000-10-04,cal,3890,-2880,14.3,52.82,32.6,11.71,-2.39,-44.93,1.91,27.96,9.56,-0.46,0
Xe,Xe,Xe,aq,PS01.1,NA,2000-10-04,cal,3215,-4540,14.5,64.77,42.5,18.4,-2.39,-59.03,1.43,35.85,13.86,-0.39,0
-CH4,NA,CH4,aq,PS01.1,NA,2000-10-04,cal,-8140,-20930,21,60.23,36,17.69,-15.3,-67.88,11.47,40.87,6.45,-0.4,0
CO2,NA,CO2,aq,PS01.1,NA,2005-08-18,cal,-92250,-98900,28.1,51.86,33.5,15.2964,-10.0382,-55.4493,7.4092,36.8069,3.5851,-0.3107,0
CF4,NA,CF4,aq,SSW01,NA,2006-09-01,cal,-202700,-224680,32.4,105.4,0,0,0,0,0,51.2936,28.0572,-0.3282,0
SF6,NA,SF6,aq,SSW01,NA,2006-09-01,cal,-259240,-293780,37.2,146.4,0,0,0,0,0,61.295,40.7143,-0.2601,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_gas.csv 2022-04-11 02:27:40 UTC (rev 721)
@@ -1,6 +1,5 @@
name,abbrv,formula,state,ref1,ref2,date,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
argon,Ar,Ar,gas,WEP+82,Kel60,1989-12-27,cal,0,0,37.008,NA,0,4.968,0,0,0,0,0,0,8000
-methane,CH4,CH4,gas,WEP+82,Kel60,1987-12-15,cal,-12122.4,-17880,44.518,NA,0,5.65,11.44,-0.46,0,0,0,0,1500
"carbon dioxide",CO2,CO2,gas,WEP+82,Kel60,1989-12-27,cal,-94254,-94051,51.085,NA,0,10.57,2.1,-2.06,0,0,0,0,2500
hydrogen,H2,H2,gas,WEP+82,Kel60,1989-12-27,cal,0,0,31.234,NA,0,6.52,0.78,0.12,0,0,0,0,3000
"hydrogen sulfide",H2S,H2S,gas,WEP+82,Kel60,1989-12-27,cal,-8021,-4931,49.185,NA,0,7.81,2.96,-0.46,0,0,0,0,2300
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv 2022-04-11 02:27:40 UTC (rev 721)
@@ -1,4 +1,5 @@
name,abbrv,formula,state,ref1,ref2,date,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+CH4,NA,CH4,aq,PS01,NA,2000-10-04,cal,-8140,-20930,21,60.23,36,17.69,-15.3,-67.88,11.47,40.87,6.45,-0.4,0
ethane,NA,C2H6,aq,SH90,NA,1987-08-31,cal,-3886,-24650,26.81,88.3,51.3,8.634,13.3011,0.5205,-3.3288,54.1755,14.9521,-0.406,0
propane,NA,C3H8,aq,SH90,NA,1987-08-31,cal,-1963,-30490,33.37,110.6,67,10.7625,18.4948,-1.5133,-3.5435,66.3294,19.4946,-0.5053,0
butane,NA,C4H10,aq,SH90,NA,1993-01-15,cal,36,-36230,40.02,133.9,82.8,12.8905,23.696,-3.5683,-3.7585,79.0569,24.2408,-0.6061,0
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_gas.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_gas.csv 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_gas.csv 2022-04-11 02:27:40 UTC (rev 721)
@@ -1,4 +1,5 @@
name,abbrv,formula,state,ref1,ref2,date,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+methane,CH4,CH4,gas,WEP+82,Kel60,1987-12-15,cal,-12122.4,-17880,44.518,NA,0,5.65,11.44,-0.46,0,0,0,0,1500
"carbon monoxide",CO,CO,gas,Sho93.1,NA,1993-03-18,cal,-32784,-26416,47.245,6.965,0,6.79,0.98,-0.11,0,0,0,0,5000
ethylene,C2H4,C2H4,gas,Sho93.1,NA,1993-09-22,cal,16280,12500,52.45,10.41,0,8.35,0.15,-2.29,0,0,0,0,1000
phenol,C6H6O,C6H6O,gas,DSM+97.1,NA,1997-11-20,cal,-7860,-23030,75.4,24.5,0,30.424,27.016,-12.431,0,0,0,0,1000
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2022-04-11 02:27:40 UTC (rev 721)
@@ -123,7 +123,7 @@
AZ01,"N. N. Akinfiev and A. V. Zotov",2001,"Geochem. Int. 39, 990-1006","M<sup>+</sup>, MCl<sub>2</sub><sup>-</sup>, M(OH)<sub>2</sub><sup>-</sup>, MCl, and MOH (M = Au<sup>+</sup>, Ag<sup>+</sup>, or Cu<sup>+</sup>)",http://pleiades.online/cgi-perl/search.pl?type=abstract&name=geochem&number=10&year=1&page=990
MVT01,"L. Mercury, P. Vieillard. and Y. Tardy",2001,"Appl. Geochem. 16, 161-181","polymorphs of ice",https://doi.org/10.1016/S0883-2927(00)00025-1
PS01,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes (organic species)",https://doi.org/10.1016/S0016-7037(01)00678-0
-PS01.1,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes (Ar, Xe, CH<sub>4</sub>, and CO<sub>2</sub>)",https://doi.org/10.1016/S0016-7037(01)00678-0
+PS01.1,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","aqueous nonelectrolytes (Ar, Xe, and CO<sub>2</sub>)",https://doi.org/10.1016/S0016-7037(01)00678-0
Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",https://doi.org/10.1016/S0016-7037(01)00761-X
Ste01,"A. Stefansson",2001,"Chem. Geol. 172, 225-250","aqueous H<sub>4</sub>SiO<sub>4</sub>",https://doi.org/10.1016/S0009-2541(00)00263-1
SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
Modified: pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/inst/extdata/adds/OBIGT_check.csv 2022-04-11 02:27:40 UTC (rev 721)
@@ -103,30 +103,30 @@
"OBIGT",704,"RhO+","aq","cal",,,-2676
"OBIGT",705,"Ar","aq","cal",-1.24,-8.59,
"OBIGT",706,"Xe","aq","cal",2.8,,
-"OBIGT",707,"CH4","aq","cal",-2.61,,
-"OBIGT",708,"CO2","aq","cal",-4.94,,
-"OBIGT",709,"CF4","aq","cal",5.9,,-2329
-"OBIGT",716,"AsH3","aq","cal",-2.67,,
-"OBIGT",777,"RuCrO4+2","aq","cal",,,-4659
-"OBIGT",799,"AgCl","aq","cal",,-1.88,
-"OBIGT",800,"AgCl2-","aq","cal",1.65,,
-"OBIGT",801,"AgCl3-2","aq","cal",,,-546
-"OBIGT",805,"CuHS","aq","cal",7.35,-16.2,
-"OBIGT",813,"ZnO2-2","aq","cal",,-1.17,
-"OBIGT",839,"S3-","aq","cal",,,661
-"OBIGT",844,"CoCl2(tet)","aq","cal",2.81,,
-"OBIGT",845,"CoCl4-2","aq","cal",1.33,-1.19,
-"OBIGT",854,"Fe(CO3)2-2","aq","cal",,,-4792
-"OBIGT",855,"Zn(CO3)2-2","aq","cal",,,-4724
-"OBIGT",856,"Cu(CO3)2-2","aq","cal",,,-4929
-"OBIGT",857,"Pb(CO3)2-2","aq","cal",,,-6676
-"OBIGT",859,"KCO3-","aq","cal",,,4996
-"OBIGT",861,"RbCO3-","aq","cal",,,-533
-"OBIGT",864,"MnHCO3+","aq","cal",,,945
-"OBIGT",872,"KHCO3","aq","cal",,,3759
-"OBIGT",877,"NbO3-","aq","cal",-1.51,,
-"OBIGT",879,"TaO3-","aq","cal",-1.61,,
-"OBIGT",883,"HTaO3F-","aq","cal",-1.15,-1.91,
+"OBIGT",707,"CO2","aq","cal",-4.94,,
+"OBIGT",708,"CF4","aq","cal",5.9,,-2329
+"OBIGT",715,"AsH3","aq","cal",-2.67,,
+"OBIGT",776,"RuCrO4+2","aq","cal",,,-4659
+"OBIGT",798,"AgCl","aq","cal",,-1.88,
+"OBIGT",799,"AgCl2-","aq","cal",1.65,,
+"OBIGT",800,"AgCl3-2","aq","cal",,,-546
+"OBIGT",804,"CuHS","aq","cal",7.35,-16.2,
+"OBIGT",812,"ZnO2-2","aq","cal",,-1.17,
+"OBIGT",838,"S3-","aq","cal",,,661
+"OBIGT",843,"CoCl2(tet)","aq","cal",2.81,,
+"OBIGT",844,"CoCl4-2","aq","cal",1.33,-1.19,
+"OBIGT",853,"Fe(CO3)2-2","aq","cal",,,-4792
+"OBIGT",854,"Zn(CO3)2-2","aq","cal",,,-4724
+"OBIGT",855,"Cu(CO3)2-2","aq","cal",,,-4929
+"OBIGT",856,"Pb(CO3)2-2","aq","cal",,,-6676
+"OBIGT",858,"KCO3-","aq","cal",,,4996
+"OBIGT",860,"RbCO3-","aq","cal",,,-533
+"OBIGT",863,"MnHCO3+","aq","cal",,,945
+"OBIGT",871,"KHCO3","aq","cal",,,3759
+"OBIGT",876,"NbO3-","aq","cal",-1.51,,
+"OBIGT",878,"TaO3-","aq","cal",-1.61,,
+"OBIGT",882,"HTaO3F-","aq","cal",-1.15,-1.91,
+"OBIGT",884,"CH4","aq","cal",-2.61,,
"OBIGT",889,"hexane","aq","cal",1.43,3.21,
"OBIGT",892,"ethylene","aq","cal",6.12,-3.82,
"OBIGT",916,"propanol","aq","cal",-1.89,,
Modified: pkg/CHNOSZ/inst/extdata/thermo/stoich.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/vignettes/OBIGT.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/vignettes/OBIGT.Rmd 2022-04-11 02:27:40 UTC (rev 721)
@@ -244,10 +244,6 @@
<div id="D-aqueous-inorganic" style="display: none">
## <a id="aqueous-inorganic" class="anchor"></a> `r setfile("inorganic_aq.csv")`
-*Disclaimer*: To make the database easier to maintain, inorganic and organic species have been placed into separate data files, but some ambiguities surround the usage of these *-ic* words in different contexts.
-In particular, while CH<sub>4</sub> (methane) is classified in chemistry as an organic compound, in nature it can be derived from living organisms or formed abiotically [@ES13] -- that is, through inorganic processes.
-For practical reasons, CH<sub>4</sub> is placed in the "inorganic" data files in OBIGT simply so that the database can be pruned of organic compounds *except* CH<sub>4</sub> by running `OBIGT(no.organics = TRUE)`.
-The ability to remove hundreds of more complex organic compounds while keeping CH<sub>4</sub> is useful for some models of inorganic reactions in hydrothermal systems.
```{r reflist, results="asis", echo=FALSE}
```
Modified: pkg/CHNOSZ/vignettes/OBIGT.bib
===================================================================
--- pkg/CHNOSZ/vignettes/OBIGT.bib 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/vignettes/OBIGT.bib 2022-04-11 02:27:40 UTC (rev 721)
@@ -1766,14 +1766,3 @@
volume = {317},
doi = {10.2475/07.2017.01},
}
-
- at Article{ES13,
- author = {Etiope, Giuseppe and Sherwood Lollar, Barbara},
- journal = {Reviews of Geophysics},
- title = {Abiotic methane on {E}arth},
- year = {2013},
- number = {2},
- pages = {276--299},
- volume = {51},
- doi = {10.1002/rog.20011},
-}
Modified: pkg/CHNOSZ/vignettes/customizing.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/customizing.Rmd 2022-04-09 09:26:30 UTC (rev 720)
+++ pkg/CHNOSZ/vignettes/customizing.Rmd 2022-04-11 02:27:40 UTC (rev 721)
@@ -175,7 +175,7 @@
The state can be one of `aq`, `gas`, or `cr`.
For minerals with higher-temperature polymorphs, they are named `cr2`, `cr3`, etc.
`r NOTE`: `cr` stands for "crystalline"; this naming convention (which was inherited from SUPCRT92 data files) refers to any solid phases including amorphous SiO<sub>2</sub> and other minerals.
-- A chemical `r formula` is required to do almost anything useful in CHNOSZ (e.g. check reaction balancing with `r subcrt_` and add species with `r basis_` or `r species_`). `r NOTE`: The convention has been adopted that the `r name` of aqueous species in OBIGT is the same as the chemical formula. Most minerals, gases, and liquids have a `r name` that is a common name.
+- A chemical `r formula` is required to do almost anything useful in CHNOSZ (e.g. check reaction balancing with `r subcrt_` and add species with `r basis_` or `r species_`). `r NOTE`: The `r name` of *inorganic* aqueous species *and CH<sub>4</sub>* in OBIGT is the same as the chemical formula. Most minerals, gases, liquids, and organic aqueous species have a `r name` that is a common name. This permits a shortcut to identify commonly used species in `r subcrt_`: `O2` without a state refers to dissolved oxygen, while `oxygen` refer to the gas.
- Likewise, `E_units` needs to be specified to perform any calculations of thermodynamic properties. The value can be `J` for Joules or `cal` for calories.
OPTIONAL: Everything else.
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