[CHNOSZ-commits] r562 - in pkg/CHNOSZ: . R inst man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jul 15 09:28:56 CEST 2020
Author: jedick
Date: 2020-07-15 09:28:56 +0200 (Wed, 15 Jul 2020)
New Revision: 562
Added:
pkg/CHNOSZ/vignettes/multi_metal.Rmd
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/mosaic.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/mosaic.Rd
pkg/CHNOSZ/vignettes/vig.bib
Log:
Add multi_metal.Rmd vignette
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2020-07-15 03:39:52 UTC (rev 561)
+++ pkg/CHNOSZ/DESCRIPTION 2020-07-15 07:28:56 UTC (rev 562)
@@ -1,6 +1,6 @@
Date: 2020-07-15
Package: CHNOSZ
-Version: 1.3.6-35
+Version: 1.3.6-36
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/mosaic.R
===================================================================
--- pkg/CHNOSZ/R/mosaic.R 2020-07-15 03:39:52 UTC (rev 561)
+++ pkg/CHNOSZ/R/mosaic.R 2020-07-15 07:28:56 UTC (rev 562)
@@ -42,7 +42,7 @@
hasbases2 <- TRUE
}
otherargs <- list(...)
- allargs <- c(list(bases = bases, blend = blend), otherargs)
+ allargs <- c(list(bases = bases, blend = blend, predominant = predominant), otherargs)
out <- do.call(mosaic, allargs)
# replace A.bases (affinity calculations for all groups of basis species) with backwards-compatbile A.bases and A.bases2
if(hasbases2) A.bases2 <- out$A.bases[[2]]
@@ -109,9 +109,9 @@
# calculate equilibrium mole fractions for each group of basis species
group.fraction <- list()
blend <- rep(blend, length(A.bases))
+ E.bases <- list()
for(i in 1:length(A.bases)) {
- if(blend[i]) {
- E.bases <- list()
+ if(blend[i] & is.null(predominant[i][[1]])) {
# this isn't needed (and doesn't work) if all the affinities are NA 20180925
if(any(!sapply(A.bases[[1]]$values, is.na))) {
# 20190504: when equilibrating the changing basis species, use a total activity equal to the activity from the basis definition
@@ -188,6 +188,5 @@
# for argument recall, include all arguments in output 20190120
allargs <- c(list(bases = bases, blend = blend), list(...))
# return the affinities for the species and basis species
- if(any(blend)) return(list(fun = "mosaic", args = allargs, A.species = A.species, A.bases = A.bases, E.bases = E.bases))
- else return(list(fun = "mosaic", args = allargs, A.species = A.species, A.bases = A.bases))
+ return(list(fun = "mosaic", args = allargs, A.species = A.species, A.bases = A.bases, E.bases = E.bases))
}
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2020-07-15 03:39:52 UTC (rev 561)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2020-07-15 07:28:56 UTC (rev 562)
@@ -5,7 +5,7 @@
% macros
\newcommand{\H2O}{\ifelse{latex}{\eqn{\mathrm{H_{2}O}}}{\ifelse{html}{\out{H<sub>2</sub>O}}{H2O}}}
-\section{Changes in CHNOSZ version 1.3.6-35 (2020-07-15)}{
+\section{Changes in CHNOSZ version 1.3.6-36 (2020-07-15)}{
\subsection{MAJOR CHANGES}{
\itemize{
@@ -74,6 +74,9 @@
\subsection{DEMOS AND VIGNETTES}{
\itemize{
+ \item Add \samp{multi_metal.Rmd} for examples of diagrams with multiple
+ metals.
+
\item Add \samp{demo/comproportionation.R}: Gibbs energy of sulfur
comproportionation, after
\href{https://doi.org/10.1111/1462-2920.14982}{Amend et al., 2020}.
Modified: pkg/CHNOSZ/man/mosaic.Rd
===================================================================
--- pkg/CHNOSZ/man/mosaic.Rd 2020-07-15 03:39:52 UTC (rev 561)
+++ pkg/CHNOSZ/man/mosaic.Rd 2020-07-15 07:28:56 UTC (rev 562)
@@ -37,10 +37,12 @@
If \code{blend} is FALSE, the function returns the affinities calculated using the single predominant basis species in \code{bases} at each condition.
This is appropriate when minerals, rather than aqueous species, are used as the changing basis species.
-Note, however, that \code{mosaic} is not internally recursive: the predominances of one group of basis species (e.g. minerals) do not take account of changes in another group (e.g. aqueous species).
-This limitation can be overcome by supplying the calculated predominances (from the \code{predominant} element of the output of \code{\link{diagram}}) in the appropriate position (for that group of basis species) in the \code{predominant} argument.
+Note, however, that \code{mosaic} is not internally recursive: the predominances of one group of basis species (e.g. minerals) are not affected by changes in another group (e.g. aqueous species).
+
+This limitation can be overcome by supplying the calculated predominances (from the \code{predominant} element of the output of \code{\link{diagram}}) as an element of the list in the \code{predominant} argument whose position corresponds to the appropriate group of basis species.
By using the predominances of minerals in one calculation to identify the basis species in a subsequent calculation, a series of linked \code{mosaic} diagrams with increasing complexity can be made.
This is useful for diagrams for minerals with multiple metallic elements.
+Note that a value in any position of the \code{predominant} list forces \code{blend = FALSE} for the corresponding group of basis species, so there is no need to explicity change the \code{blend} argument.
A more flexible method of specifying multiple sets of basis species is now available.
Instead of using \code{bases} and \code{bases2}, supply a list for just the \code{bases} argument.
Added: pkg/CHNOSZ/vignettes/multi_metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi_metal.Rmd (rev 0)
+++ pkg/CHNOSZ/vignettes/multi_metal.Rmd 2020-07-15 07:28:56 UTC (rev 562)
@@ -0,0 +1,158 @@
+---
+title: "Diagrams with multiple metals"
+author: "Jeffrey M. Dick"
+output:
+ html_vignette:
+ mathjax: null
+vignette: >
+ %\VignetteIndexEntry{Diagrams with multiple metals}
+ %\VignetteEngine{knitr::rmarkdown}
+ %\VignetteEncoding{UTF-8}
+bibliography: vig.bib
+csl: elementa.csl
+---
+<style>
+/* https://gomakethings.com/how-to-break-an-image-out-of-its-parent-container-with-css/ */
+ at media (min-width: 700px) {
+ .full-width {
+ left: 50%;
+ margin-left: -50vw;
+ margin-right: -50vw;
+ max-width: 100vw;
+ position: relative;
+ right: 50%;
+ width: 100vw;
+ }
+}
+ at media (min-width: 1020px) {
+ .full-width {
+ left: 50vw; /* fallback if needed */
+ left: calc(50vw - 160px);
+ width: 1000px;
+ position: relative;
+ background-color: #9ecff7;
+ padding:10px;
+ }
+}
+/* zero margin around pre blocks (looks more like R console output) */
+pre {
+ margin-top: 0;
+ margin-bottom: 0;
+}
+</style>
+<script>
+function ToggleDiv(ID) {
+ var D = document.getElementById("D-" + ID);
+ var B = document.getElementById("B-" + ID);
+ if (D.style.display === "none") {
+ // open the div and change button text
+ D.style.display = "block";
+ B.innerText = "Hide code";
+ } else {
+ // close the div and change button text
+ D.style.display = "none";
+ B.innerText = "Show code";
+ }
+}
+</script>
+
+```{r setup, include=FALSE}
+## use pngquant to optimize PNG images
+library(knitr)
+knit_hooks$set(pngquant = hook_pngquant)
+pngquant <- "--speed=1 --quality=0-25"
+if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL
+```
+
+```{r CHNOSZ_reset, include=FALSE}
+library(CHNOSZ)
+reset()
+```
+
+This vignette was compiled on `r Sys.Date()` with CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
+
+Basic diagrams in CHNOSZ are made for reactions that are *balanced on an element* (see [Equilibrium in CHNOSZ](equilibrium.html)) and therefore represent minerals or aqueous species that all have one element, often a metal, in common.
+This vignette describes some methods for constructing diagrams for elements with multiple metals.
+The methods are **simple overlay**, **mosaic series**, and **secondary balancing**.
+
+## Simple Overlay
+
+Simple overlay refers to independent calculations for two different systems that are displayed on the same diagram.
+It is easy to make such a diagram, but there is no interaction between the systems.
+
+## Mosaic Series
+
+A mosaic diagram shows the effects of changing basis species on the stabilities of minerals.
+The Fe-S-O-H system is a common example: the speciation of aqueous sulfur species affects the stabilities of iron oxides and sulfides.
+A mosaic series is when predominance fields for minerals calculated in one mosaic diagram are used as input to a second mosaic diagram, where the minerals are now themselves basis species.
+The example here shows the construction of a Cu-Fe-S-O-H diagram.
+
+First we define the conditions and basis species.
+It is important to put Cu^+^ first so that it will be used as the balance for the reactions with Cu-bearing minerals (which also have Fe).
+Pyrite is chosen as the starting Fe-bearing basis species, which will be changed as indicated in `bases2`.
+
+```{r mosaic1, results = "hide", message = FALSE}
+logaH2S <- -2
+T <- 200
+pH <- c(0, 12, 500)
+O2 <- c(-50, -30, 500)
+basis(c("Cu+", "pyrite", "H2S", "oxygen", "H2O", "H+"))
+basis("H2S", logaH2S)
+bases1 <- c("H2S", "HS-", "HSO4-", "SO4-2")
+bases2 <- c("pyrite", "pyrrhotite", "magnetite", "hematite")
+```
+
+Now we calculate affinities for minerals in the Fe-S-O-H system using changing aqueous sulfur species in `bases1`.
+The result is used to make different layers of the diagram:
+
+1. Water stability region (bounded by the grey area)
+2. Predominance fields for the aqueous S species (italic blue text and dashed lines)
+3. Stability areas for the Fe-bearing minerals (black text and solid lines)
+
+```{r mosaic2, eval = FALSE, echo = 1:6}
+species(bases2)
+mFe <- mosaic(bases1, pH = pH, O2 = O2, T = T)
+diagram(mFe$A.bases, lty = 0, names = NA)
+diagram(mFe$A.bases, lty = 2, col = 4, col.names = 4,
+ italic = TRUE, add = TRUE, limit.water = FALSE)
+dFe <- diagram(mFe$A.species, add = TRUE, limit.water = FALSE)
+species(c("chalcopyrite", "bornite"))
+mCu <- mosaic(list(bases1, bases2), pH = pH, O2 = O2,
+ T = T, predominant = list(NULL, dFe$predominant))
+diagram(mCu$A.species, add = TRUE, col = 2, col.names = 2,
+ lwd = 2, bold = TRUE, limit.water = FALSE)
+TP <- describe.property(c("T", "P"), c(T, "Psat"))
+legend("topright", TP, bty = "n")
+title(paste("Cu-Fe-S-O-H; Total S =", 10^logaH2S, "m"))
+```
+
+Next we load the Cu-bearing minerals and calculate their affinities while changing *both* the aqueous sulfur species and the Fe-bearing minerals whose stability fields were just calculated.
+The result is used to plot the final layer of the diagram:
+
+4. Stability areas for Cu-bearing minerals (bold red text and solid lines)
+
+After that we add the legend and title.
+
+```{r mosaic2, echo=7:14, results = "hide", message = FALSE, fig.width = 6, fig.height = 5, out.width = "80%", fig.align = "center", pngquant = pngquant}
+```
+
+This diagram has a distinctive chalcopyrite "hook" that is controlled on the low-pH side by the reaction with pyrite.
+Usually only that reaction is shown in published diagrams [e.g. @And75;@Gio02], but diagrams with a similar chalcopyrite wedge or hook can be seen in @BBR77.
+
+## Secondary Balancing
+
+Predominance diagrams in CHNOSZ are made using the maximum affinity method, where the affinities of formation reactions of species are divided by the *balancing coefficients* [@Dic19].
+Usually, these balancing coefficients are taken from the formation reactions themselves; for example, if they are the coefficients on the Fe-bearing basis species, then the reactions are said to be "balanced on Fe".
+
+Some diagrams in the literature are made with secondary balancing constraints in addition to the primary ones.
+For example, reactions of Fe-bearing minerals are balanced on Fe, and reactions of Cu-bearing minerals are balanced on Cu; these are both primary balancing coefficients.
+Then, reactions between all minerals are balanced on H^+^ as the secondary balancing coefficients.
+The challenge is to implement the secondary balance while also maintining the primary balance; such a method has been implemented in `bimetal()` function.
+
+TODO: add example.
+
+## Document history
+
+* 2020-07-15 First version.
+
+## References
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2020-07-15 03:39:52 UTC (rev 561)
+++ pkg/CHNOSZ/vignettes/vig.bib 2020-07-15 07:28:56 UTC (rev 562)
@@ -1,4 +1,3 @@
-% Encoding: UTF-8
@Article{AD01,
author = {Aksu, Serdar and Doyle, Fiona M.},
@@ -31,15 +30,6 @@
doi = {10.1016/S0301-4622(00)00116-2},
}
- at Book{BPJ85,
- author = {Bard, A. J. and Parsons, R. and Jordan, J.},
- publisher = {M. Dekker},
- title = {{S}tandard {P}otentials in {A}queous {S}olution},
- year = {1985},
- address = {New York},
- url = {http://www.worldcat.org/oclc/12106344},
-}
-
@Article{BZA10,
author = {Bazarkina, E. F. and Zotov, A. V. and Akinfiev, N. N.},
journal = {Geology of Ore Deposits},
@@ -101,21 +91,21 @@
@Article{Dic09,
author = {Dick, Jeffrey M.},
journal = {BMC Systems Biology},
- title = {{C}alculation of the relative metastabilities of proteins in subcellular compartments of \emph{Saccharomyces cerevisiae}},
+ title = {{C}alculation of the relative metastabilities of proteins in subcellular compartments of \emph{{S}accharomyces cerevisiae}},
year = {2009},
+ pages = {75},
volume = {3},
- pages = {75},
doi = {10.1186/1752-0509-3-75},
}
@Article{Dic14,
- author = {Dick, Jeffrey M.},
- journal = {Journal of the Royal Society Interface},
- title = {{A}verage oxidation state of carbon in proteins},
- year = {2014},
- volume = {11},
- pages = {20131095},
- doi = {10.1098/rsif.2013.1095},
+ author = {Dick, Jeffrey M.},
+ journal = {Journal of the Royal Society Interface},
+ title = {{A}verage oxidation state of carbon in proteins},
+ year = {2014},
+ volume = {11},
+ pages = {20131095},
+ doi = {10.1098/rsif.2013.1095},
}
@Article{Dic15,
@@ -127,14 +117,14 @@
}
@Article{DLH06,
- author = {Dick, Jeffrey M. and LaRowe, Douglas E. and Helgeson, Harold C.},
- journal = {Biogeosciences},
- title = {{T}emperature, pressure, and electrochemical constraints on protein speciation: {G}roup additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins},
- year = {2006},
- volume = {3},
- number = {3},
- pages = {311--336},
- doi = {10.5194/bg-3-311-2006},
+ author = {Dick, Jeffrey M. and LaRowe, Douglas E. and Helgeson, Harold C.},
+ journal = {Biogeosciences},
+ title = {{T}emperature, pressure, and electrochemical constraints on protein speciation: {G}roup additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins},
+ year = {2006},
+ number = {3},
+ pages = {311--336},
+ volume = {3},
+ doi = {10.5194/bg-3-311-2006},
}
@Article{DS11,
@@ -204,13 +194,13 @@
}
@Article{HDNB78,
- author = {Helgeson, Harold C. and Delany, Joan M. and Nesbitt, H. Wayne and Bird, Dennis K.},
- journal = {American Journal of Science},
- title = {{S}ummary and critique of the thermodynamic properties of rock-forming minerals},
- year = {1978},
- volume = {278A},
- pages = {1--229},
- url = {http://www.worldcat.org/oclc/13594862},
+ author = {Helgeson, Harold C. and Delany, Joan M. and Nesbitt, H. Wayne and Bird, Dennis K.},
+ journal = {American Journal of Science},
+ title = {{S}ummary and critique of the thermodynamic properties of rock-forming minerals},
+ year = {1978},
+ pages = {1--229},
+ volume = {278A},
+ url = {http://www.worldcat.org/oclc/13594862},
}
@Article{HKF81,
@@ -218,9 +208,9 @@
journal = {American Journal of Science},
title = {{T}heoretical prediction of the thermodynamic behavior of aqueous electrolytes at high pressures and temperatures: {IV}. {C}alculation of activity coefficients, osmotic coefficients, and apparent molal and standard and relative partial molal properties to 600°{C} and 5 {K}b},
year = {1981},
- volume = {281},
number = {10},
pages = {1249--1516},
+ volume = {281},
doi = {10.2475/ajs.281.10.1249},
size = {268 p.},
}
@@ -230,32 +220,31 @@
journal = {Computers \& Geosciences},
title = {{SUPCRT}92: {A} software package for calculating the standard molal thermodynamic properties of minerals, gases, aqueous species, and reactions from 1 to 5000 bar and 0 to 1000°{C}},
year = {1992},
- volume = {18},
number = {7},
pages = {899--947},
+ volume = {18},
doi = {10.1016/0098-3004(92)90029-Q},
}
@Article{Kit14,
- author = {Kitadai, Norio},
- journal = {Journal of Molecular Evolution},
- title = {{T}hermodynamic prediction of glycine polymerization as a function of temperature and p{H} consistent with experimentally obtained results},
- year = {2014},
- volume = {78},
- number = {3-4},
- pages = {171--187},
- doi = {10.1007/s00239-014-9616-1},
- issn = {0022-2844},
+ author = {Kitadai, Norio},
+ journal = {Journal of Molecular Evolution},
+ title = {{T}hermodynamic prediction of glycine polymerization as a function of temperature and p{H} consistent with experimentally obtained results},
+ year = {2014},
+ number = {3-4},
+ pages = {171--187},
+ volume = {78},
+ doi = {10.1007/s00239-014-9616-1},
}
@Article{LD12,
- author = {LaRowe, Douglas E. and Dick, Jeffrey M.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the standard molal thermodynamic properties of crystalline peptides},
- year = {2012},
- volume = {80},
- pages = {70--91},
- doi = {10.1016/j.gca.2011.11.041},
+ author = {LaRowe, Douglas E. and Dick, Jeffrey M.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{C}alculation of the standard molal thermodynamic properties of crystalline peptides},
+ year = {2012},
+ pages = {70--91},
+ volume = {80},
+ doi = {10.1016/j.gca.2011.11.041},
}
@Article{LH06a,
@@ -294,14 +283,14 @@
}
@Article{MSS13,
- author = {Manning, Craig E. and Shock, Everett L. and Sverjensky, Dimitri A.},
- journal = {Reviews in Mineralogy and Geochemistry},
- title = {{T}he chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: {E}xperimental and theoretical constraints},
- year = {2013},
- volume = {75},
- number = {1},
- pages = {109--148},
- doi = {10.2138/rmg.2013.75.5},
+ author = {Manning, Craig E. and Shock, Everett L. and Sverjensky, Dimitri A.},
+ journal = {Reviews in Mineralogy and Geochemistry},
+ title = {{T}he chemistry of carbon in aqueous fluids at crustal and upper-mantle conditions: {E}xperimental and theoretical constraints},
+ year = {2013},
+ number = {1},
+ pages = {109--148},
+ volume = {75},
+ doi = {10.2138/rmg.2013.75.5},
}
@InProceedings{NPW_79,
@@ -345,10 +334,9 @@
journal = {Earth and Planetary Science Letters},
title = {{S}tability and abundance of the trisulfur radical ion in hydrothermal fluids},
year = {2015},
+ pages = {298--309},
volume = {411},
- pages = {298--309},
doi = {10.1016/j.epsl.2014.11.035},
- issn = {0012-821X},
}
@Book{Pou49,
@@ -396,14 +384,14 @@
}
@Article{SB01,
- author = {Schafer, Freya Q. and Buettner, Garry R.},
- journal = {Free Radical Biology and Medicine},
- title = {Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple},
- year = {2001},
- volume = {30},
- number = {11},
- pages = {1191--1212},
- doi = {10.1016/S0891-5849(01)00480-4},
+ author = {Schafer, Freya Q. and Buettner, Garry R.},
+ journal = {Free Radical Biology and Medicine},
+ title = {{R}edox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple},
+ year = {2001},
+ volume = {30},
+ number = {11},
+ pages = {1191--1212},
+ doi = {10.1016/S0891-5849(01)00480-4},
}
@Article{SS95,
@@ -465,14 +453,14 @@
}
@Article{SH90,
- author = {Shock, Everett L. and Helgeson, Harold C.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {S}tandard partial molal properties of organic species},
- year = {1990},
- volume = {54},
- number = {4},
- pages = {915--945},
- doi = {10.1016/0016-7037(90)90429-O},
+ author = {Shock, Everett L. and Helgeson, Harold C.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {S}tandard partial molal properties of organic species},
+ year = {1990},
+ number = {4},
+ pages = {915--945},
+ volume = {54},
+ doi = {10.1016/0016-7037(90)90429-O},
}
@Article{SHS89,
@@ -514,8 +502,8 @@
journal = {Chemical Geology},
title = {{D}issolution of primary minerals of basalt in natural waters. {I}. {C}alculation of mineral solubilities from 0°{C} to 350°{C}},
year = {2001},
+ pages = {225--250},
volume = {172},
- pages = {225--250},
doi = {10.1016/S0009-2541(00)00263-1},
}
@@ -524,10 +512,9 @@
journal = {Geochimica et Cosmochimica Acta},
title = {{W}ater in the deep {E}arth: {T}he dielectric constant and the solubilities of quartz and corundum to 60 kb and 1,200 °{C}},
year = {2014},
+ pages = {125--145},
volume = {129},
- pages = {125--145},
doi = {10.1016/j.gca.2013.12.019},
- issn = {0016-7037},
}
@Article{SSH97,
@@ -535,21 +522,21 @@
journal = {Geochimica et Cosmochimica Acta},
title = {{P}rediction of the thermodynamic properties of aqueous metal complexes to 1000°{C} and 5 kb},
year = {1997},
- volume = {61},
number = {7},
pages = {1359--1412},
+ volume = {61},
doi = {10.1016/S0016-7037(97)00009-4},
}
@Article{TS01,
- author = {Tagirov, Boris and Schott, Jacques},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{A}luminum speciation in crustal fluids revisited},
- year = {2001},
- volume = {65},
- number = {21},
- pages = {3965--3992},
- doi = {10.1016/S0016-7037(01)00705-0},
+ author = {Tagirov, Boris and Schott, Jacques},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{A}luminum speciation in crustal fluids revisited},
+ year = {2001},
+ number = {21},
+ pages = {3965--3992},
+ volume = {65},
+ doi = {10.1016/S0016-7037(01)00705-0},
}
@Article{TH88,
@@ -568,9 +555,9 @@
journal = {Journal of Physical and Chemical Reference Data},
title = {{T}he {IAPWS} formulation 1995 for the thermodynamic properties of ordinary water substance for general and scientific use},
year = {2002},
- volume = {31},
number = {2},
pages = {387--535},
+ volume = {31},
doi = {10.1063/1.1461829},
}
@@ -586,27 +573,14 @@
issn = {0021-9606},
}
- at Article{WE08,
- author = {Wu, Martin and Eisen, Jonathan A.},
- journal = {Genome Biology},
- title = {{A} simple, fast, and accurate method of phylogenomic inference},
- year = {2008},
- volume = {9},
- number = {10},
- pages = {R151},
- doi = {10.1186/gb-2008-9-10-r151},
- issn = {1474-760X},
-}
-
@Article{ZZL_16,
- author = {Kurt Zimmer and Yilun Zhang and Peng Lu and Yanyan Chen and Guanru Zhang and Mehmet Dalkilic and Chen Zhu},
- journal = {Computers \& Geosciences},
- title = {{SUPCRTBL}: {A} revised and extended thermodynamic dataset and software package of {SUPCRT}92},
- year = {2016},
- volume = {90},
- pages = {97--111},
- doi = {10.1016/j.cageo.2016.02.013},
- issn = {0098-3004},
+ author = {Kurt Zimmer and Yilun Zhang and Peng Lu and Yanyan Chen and Guanru Zhang and Mehmet Dalkilic and Chen Zhu},
+ journal = {Computers \& Geosciences},
+ title = {{SUPCRTBL}: {A} revised and extended thermodynamic dataset and software package of {SUPCRT}92},
+ year = {2016},
+ pages = {97--111},
+ volume = {90},
+ doi = {10.1016/j.cageo.2016.02.013},
}
@Book{CWM89,
@@ -648,21 +622,21 @@
journal = {Geochimica et Cosmochimica Acta},
title = {{T}hermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters},
year = {2003},
- volume = {67},
number = {4},
pages = {613--629},
+ volume = {67},
doi = {10.1016/S0016-7037(02)01141-9},
}
@Article{CPCC17,
- author = {Caporuscio, F. A. and Palaich, S. E. M. and Cheshire, M. C. and Jov\'e Col\'on, C. F.},
- journal = {Journal of Nuclear Materials},
- title = {{C}orrosion of copper and authigenic sulfide mineral growth in hydrothermal bentonite experiments},
- year = {2017},
- volume = {485},
- pages = {137--146},
- doi = {10.1016/j.jnucmat.2016.12.036},
- issn = {0022-3115},
+ author = {Caporuscio, F. A. and Palaich, S. E. M. and Cheshire, M. C. and Jov\'e Col\'on, C. F.},
+ journal = {Journal of Nuclear Materials},
+ title = {{C}orrosion of copper and authigenic sulfide mineral growth in hydrothermal bentonite experiments},
+ year = {2017},
+ pages = {137--146},
+ volume = {485},
+ doi = {10.1016/j.jnucmat.2016.12.036},
+ issn = {0022-3115},
}
@Article{MDS_13,
@@ -680,8 +654,8 @@
journal = {Organic Geochemistry},
title = {Concentrations and distributions of amino acids in black and white smoker fluids at temperatures over 200 °C},
year = {2014},
+ pages = {98--106},
volume = {66},
- pages = {98--106},
doi = {10.1016/j.orggeochem.2013.11.008},
issn = {0146-6380},
}
@@ -691,9 +665,9 @@
journal = {Journal of Hydrology},
title = {{I}mplications of replacement for reaction--transport modeling},
year = {1998},
- volume = {209},
number = {1-4},
pages = {137--146},
+ volume = {209},
doi = {10.1016/S0022-1694(98)00150-4},
issn = {0022-1694},
}
@@ -731,13 +705,13 @@
}
@Article{Dic17,
- author = {Dick, Jeffrey M.},
- journal = {PeerJ},
- title = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
- year = {2017},
- volume = {5},
- pages = {e3421},
- doi = {10.7717/peerj.3421},
+ author = {Dick, Jeffrey M.},
+ journal = {PeerJ},
+ title = {{C}hemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress},
+ year = {2017},
+ pages = {e3421},
+ volume = {5},
+ doi = {10.7717/peerj.3421},
}
@Article{SVI12,
@@ -756,6 +730,16 @@
zs = {0},
}
+ at Article{Dic19,
+ author = {Dick, Jeffrey M.},
+ journal = {Frontiers in Earth Science},
+ title = {{CHNOSZ}: {T}hermodynamic calculations and diagrams for geochemistry},
+ year = {2019},
+ pages = {180},
+ volume = {7},
+ doi = {10.3389/feart.2019.00180},
+}
+
@Article{WJ17,
author = {Thomas J. Wolery and Jov\'e Col\'on, Carlos F.},
journal = {Geochimica et Cosmochimica Acta},
@@ -779,28 +763,27 @@
}
@Article{Alb96,
- author = {Alberty, Robert A.},
- journal = {European Journal of Biochemistry},
- title = {{R}ecommendations for nomenclature and tables in biochemical thermodynamics},
- year = {1996},
- volume = {240},
- number = {1},
- pages = {1--14},
- doi = {10.1111/j.1432-1033.1996.0001h.x},
- issn = {1432-1033},
- publisher = {Blackwell Science Ltd},
+ author = {Alberty, Robert A.},
+ journal = {European Journal of Biochemistry},
+ title = {{R}ecommendations for nomenclature and tables in biochemical thermodynamics},
+ year = {1996},
+ volume = {240},
+ number = {1},
+ pages = {1--14},
+ doi = {10.1111/j.1432-1033.1996.0001h.x},
+ issn = {1432-1033},
+ publisher = {Blackwell Science Ltd},
}
@Article{PAB_14,
- author = {Pokrovski, Gleb S. and Akinfiev, Nikolay N. and Borisova, Anastassia Y. and Zotov, Alexandre V. and Kouzmanov, Kalin},
- journal = {Geological Society, London, Special Publications},
- title = {{G}old speciation and transport in geological fluids: insights from experiments and physical-chemical modelling},
- year = {2014},
- volume = {402},
- number = {1},
- pages = {9--70},
- doi = {10.1144/SP402.4},
- issn = {0305-8719},
+ author = {Pokrovski, Gleb S. and Akinfiev, Nikolay N. and Borisova, Anastassia Y. and Zotov, Alexandre V. and Kouzmanov, Kalin},
+ journal = {Geological Society, London, Special Publications},
+ title = {{G}old speciation and transport in geological fluids: insights from experiments and physical-chemical modelling},
+ year = {2014},
+ number = {1},
+ pages = {9--70},
+ volume = {402},
+ doi = {10.1144/SP402.4},
}
@Article{KOSG00,
@@ -816,3 +799,36 @@
source = {Crossref},
}
+ at Article{And75,
+ author = {Anderson, G. M.},
+ journal = {Economic Geology},
+ title = {{P}recipitation of {M}ississippi {V}alley-type ores},
+ year = {1975},
+ number = {5},
+ pages = {937--942},
+ volume = {70},
+ doi = {10.2113/gsecongeo.70.5.937},
+}
+
+ at Article{Gio02,
+ author = {Giordano, Thomas H.},
+ journal = {Geochemical Transactions},
+ title = {{T}ransport of {P}b and {Z}n by carboxylate complexes in basinal ore fluids and related petroleum-field brines at 100 °{C}: the influence of p{H} and oxygen fugacity},
+ year = {2002},
+ pages = {56--72},
+ volume = {3},
+ doi = {10.1186/1467-4866-3-56},
+ sn = {1467-4866},
+ z9 = {6},
+}
+
+ at Article{BBR77,
+ author = {Barton, Paul B., Jr. and Bethke, Phillip M. and Roedder, Edwin},
+ journal = {Economic Geology},
+ title = {Environment of ore deposition in the {C}reede mining district, {S}an {J}uan {M}ountains, {C}olorado; {P}art {III}, {P}rogress toward interpretation of the chemistry of the ore-forming fluid for the {OH} {V}ein},
+ year = {1977},
+ number = {1},
+ pages = {1--24},
+ volume = {72},
+ doi = {10.2113/gsecongeo.72.1.1},
+}
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