[CHNOSZ-commits] r695 - in pkg/CHNOSZ: . R inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Feb 4 05:10:05 CET 2022
Author: jedick
Date: 2022-02-04 05:10:05 +0100 (Fri, 04 Feb 2022)
New Revision: 695
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/AkDi.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/TODO
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/multi-metal.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
Mention GEMSFIT dataset (Miron et al., 2017) in anintro.Rmd
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-02-03 13:24:57 UTC (rev 694)
+++ pkg/CHNOSZ/DESCRIPTION 2022-02-04 04:10:05 UTC (rev 695)
@@ -1,6 +1,6 @@
Date: 2022-02-03
Package: CHNOSZ
-Version: 1.4.1-20
+Version: 1.4.1-21
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/AkDi.R
===================================================================
--- pkg/CHNOSZ/R/AkDi.R 2022-02-03 13:24:57 UTC (rev 694)
+++ pkg/CHNOSZ/R/AkDi.R 2022-02-04 04:10:05 UTC (rev 695)
@@ -4,49 +4,53 @@
AkDi <- function(property = NULL, parameters = NULL, T = 298.15, P = 1, isPsat = TRUE) {
- # some constants (from Akinfiev and Diamond, 2004 doi:10.1016/j.fluid.2004.06.010)
+ # Some constants (from Akinfiev and Diamond, 2004 doi:10.1016/j.fluid.2004.06.010)
MW <- 18.0153 # g mol-1
NW <- 1000/MW # mol kg-1
R <- 8.31441 # J K-1 mol-1
- # a list for the output
+ # A list for the output
out <- list()
- # loop over species
+ # Loop over species
nspecies <- nrow(parameters)
for(i in seq_len(nspecies)) {
PAR <- parameters[i, ]
- # start with an NA-filled data frame
- myprops <- as.data.frame(matrix(NA, ncol=length(property), nrow=length(T)))
+ # Start with an NA-filled data frame
+ myprops <- as.data.frame(matrix(NA, ncol = length(property), nrow = length(T)))
colnames(myprops) <- property
- # just calculate G for now
+ # Loop over properties
for(j in seq_along(property)) {
- if(property[[j]]=="G") {
- # send a message
+ # Just calculate G for now
+ if(property[[j]] == "G") {
+ # Send a message
message("AkDi: Akinfiev-Diamond model for ", PAR$name, " gas to aq")
- # get gas properties (J mol-1)
- G_gas <- subcrt(PAR$name, "gas", T=T, P=P, convert=FALSE)$out[[1]]$G
- # TODO: does this work if E.units is cal or J?
- G_gas <- convert(G_gas, "J", T=T)
- # get H2O fugacity (bar)
- GH2O_P <- water("G", T=T, P=P)$G
- GH2O_1 <- water("G", T=T, P=1)$G
+ # Get gas properties (J mol-1)
+ G_gas <- subcrt(PAR$name, "gas", T = T, P = P, convert = FALSE)$out[[1]]$G
+ # TODO: Does this work if E.units is cal or J?
+ G_gas <- convert(G_gas, "J", T = T)
+ # Get H2O fugacity (bar)
+ GH2O_P <- water("G", T = T, P = P)$G
+ GH2O_1 <- water("G", T = T, P = 1)$G
f1 <- exp ( (GH2O_P - GH2O_1) / (1.9872 * T) )
- # for Psat, calculate the real liquid-vapor curve (not 1 bar below 100 degC)
+ # For Psat, calculate the real liquid-vapor curve (not 1 bar below 100 degC)
if(isPsat) {
P <- water("Psat", T = T, P = "Psat", P1 = FALSE)$Psat
f1[P < 1] <- P[P < 1]
}
- # density (g cm-3)
- rho1 <- water("rho", T=T, P=P)$rho / 1000
- # calculate G_hyd (J mol-1)
+ # Density (g cm-3)
+ rho1 <- water("rho", T = T, P = P)$rho / 1000
+ # Calculate G_hyd (J mol-1)
G_hyd <- R*T * ( -log(NW) + (1 - PAR$xi) * log(f1) + PAR$xi * log(10 * R * T * rho1 / MW) + rho1 * (PAR$a + PAR$b * (1000/T)^0.5) )
- # calculate the chemical potential (J mol-1)
+ # Calculate the chemical potential (J mol-1)
G <- G_gas + G_hyd
- # convert J to cal
- G <- convert(G, "cal", T=T)
- # insert into data frame of properties
+ # Convert J to cal
+ G <- convert(G, "cal", T = T)
+ # Insert into data frame of properties
myprops$G <- G
}
+ if(property[[j]] == "S") {
+ # https://stackoverflow.com/questions/11081069/calculate-the-derivative-of-a-data-function-in-r
+ }
}
out[[i]] <- myprops
}
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2022-02-03 13:24:57 UTC (rev 694)
+++ pkg/CHNOSZ/inst/CHECKLIST 2022-02-04 04:10:05 UTC (rev 695)
@@ -50,10 +50,6 @@
remove padding-top: 10px; from h2 in
rmarkdown/templates/html_vignette/resources/vignette.css
-- Documentation links: after installation, run doc/mklinks.sh
- to add links to the vignettes (for posting on the website,
- so vignettes have links to HTML renditions of Rd files)
-
***************
R compatibility
***************
@@ -77,3 +73,15 @@
- Run R_PAPERSIZE=letter R CMD Rd2pdf chnosz/
and fix any lines truncated by page margins
+
+*********************
+Vignettes for website
+*********************
+
+- Use dpi <- 72 in anintro.Rmd
+
+- Use hires <- TRUE in multi-metal.Rmd
+
+- Run doc/mklinks.sh in installed directory (adds links to HTML renditions of
+ Rd files)
+
Modified: pkg/CHNOSZ/inst/TODO
===================================================================
--- pkg/CHNOSZ/inst/TODO 2022-02-03 13:24:57 UTC (rev 694)
+++ pkg/CHNOSZ/inst/TODO 2022-02-04 04:10:05 UTC (rev 695)
@@ -48,3 +48,6 @@
[20220203]
- Allow numeric values for bases in mosaic() (test-mix.R)
+
+- Add a 'model' column to thermo()$OBIGT to indicate the thermodynamic data
+ model (e.g. HKF, CGL, Berman, AkDi, or DEW)
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2022-02-03 13:24:57 UTC (rev 694)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2022-02-04 04:10:05 UTC (rev 695)
@@ -1561,19 +1561,22 @@
browseURL(ref$URL) ## opens a link to worldcat.org
```
-## Optional data
+## Default database
Thermodynamic properties of minerals in the default database are mostly taken from @Ber88 (including silicates, aluminosilicates, calcite, dolomite, hematite, and magnetite) and @HDNB78 (native elements, sulfides, halides, sulfates, and selected carbonates and oxides that do not duplicate any in the Berman dataset).
Minerals are identified by the state `cr`, and (for the Helgeson dataset) `cr2`, `cr3`, etc. for higher-temperature polymorphs.
+Compared to SUPCRT92/SLOP98 (see below), the default database include updates for aqueous Al species [@TS01], Au species [@PAB_14] (see [<span style="color:blue">`demo(gold)`</span>](../demo)), and arsenic-bearing aqueous species and minerals, as compiled in the SUPCRTBL package [@ZZL_16].
+This list of updates is incomplete; see the vignette [<span style="color:blue">*OBIGT thermodynamic database*</span>](OBIGT.html) for a detailed list of data sources.
+
+## Optional data files
+
Some optional datasets can be activated by using <span style="color:red">`add.OBIGT()`</span>. The first couple of these contain data that have been replaced by or are incompatible with later updates; the superseded data are kept here to reproduce published calculations and for comparison with the newer data:
<span style="color:red">`add.OBIGT("SUPCRT92")`</span> -- This file contains data for minerals from SUPCRT92 (mostly Helgeson et al., 1978) that have been replaced by the Berman data set.
-<span style="color:red">`add.OBIGT("SLOP98")`</span> -- This file contains data from `slop98.dat` or later slop files, from Everett Shock's GEOPIG group at Arizona State University, that were previously used in CHNOSZ but have been replaced by newer data.
-This includes updates for aqueous Al species [@TS01], Au species [@PAB_14], and arsenic-bearing aqueous species and minerals, as compiled in the SUPCRTBL package [@ZZL_16].
+<span style="color:red">`add.OBIGT("SLOP98")`</span> -- This file contains data from `slop98.dat` or later slop files, from Everett Shock's GEOPIG group at Arizona State University, that were previously used in CHNOSZ but have been replaced by more recent data updates.
Some calculations using the older data are shown in [this vignette](#complete-equilibrium-solubility).
-See [<span style="color:blue">`demo(gold)`</span>](../demo) for calculations that depend on the data for Au species that are now loaded by default in CHNOSZ.
The updates for these data have been taken from various publications ([LaRowe and Dick, 2012](https://doi.org/10.1016/j.gca.2011.11.041); [Kitadai, 2014](https://doi.org/10.1007/s00239-014-9616-1); [Azadi et al., 2019](https://doi.org/10.1016/j.fluid.2018.10.002))
A comparison of log*K* of metal-glycinate complexes using the updated data is in [<span style="color:blue">`demo(glycinate)`</span>](../demo).
@@ -1580,6 +1583,8 @@
The next three optional datasets are provided to support newer data or models:
+<span style="color:red">`add.OBIGT("AkDi")`</span> -- These data are used in the Akinfiev-Diamond model for aqeuous nonelectrolytes [@AD03].
+
<span style="color:red">`add.OBIGT("AS04")`</span> -- This file has data for aqueous `r sio2` from @AS04 and modified HSiO<sub>3</sub><sup>-</sup>.
These data are included to help transition to the "higher solubility of quartz paradigm" [@WJ17], but are not included in the default database in order to maintain compatibility with existing data for minerals that are linked to the older aqueous `r sio2` data.
See [<span style="color:blue">`demo(aluminum)`</span>](../demo) for an example.
@@ -1588,10 +1593,8 @@
You should also run <span style="color:red">`water("DEW")`</span> to activate the equations in the model; then, they will be used by <span style="color:green">`subcrt()`</span> and <span style="color:green">`affinity()`</span>.
Examples are in [<span style="color:blue">`demo(DEW)`</span>](../demo).
-<span style="color:red">`add.OBIGT("AkDi")`</span> -- These data are used in the Akinfiev-Diamond model for aqeuous nonelectrolytes [@AD03].
+<span style="color:red">`add.OBIGT("GEMSFIT")`</span> -- This is a set of internally-conistent thermodynamic data for aqueous species in the system Ca-Mg-Na-K-Al-Si-O-H-C-Cl compiled using the GEMSFIT package [@MWKL17].
-Detailed references for these optional datasets are in the vignette [<span style="color:blue">*OBIGT thermodynamic database*</span>](OBIGT.html) (look under **Optional Data**).
-
## Adding data
You can also use <span style="color:red">`add.OBIGT()`</span> to add data from a user-specified file to the database in the current session.
Modified: pkg/CHNOSZ/vignettes/multi-metal.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/multi-metal.Rmd 2022-02-03 13:24:57 UTC (rev 694)
+++ pkg/CHNOSZ/vignettes/multi-metal.Rmd 2022-02-04 04:10:05 UTC (rev 695)
@@ -85,7 +85,7 @@
This vignette was compiled on `r Sys.Date()` with CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
-A companion paper to this vignette has been published in *Applied Computing and Geosciences* ([Dick, 2021](https://doi.org/10.1016/j.acags.2021.100059 "Diagrams with multiple metals in CHNOSZ")).
+An accompanying paper to this vignette has been published in *Applied Computing and Geosciences* ([Dick, 2021](https://doi.org/10.1016/j.acags.2021.100059 "Diagrams with multiple metals in CHNOSZ")).
Please consider citing that paper if you use the functions or diagrams described here.
The plots in this vignette were made using the following resolution settings, which can be changed if desired (low resolutions are used to save time in CRAN checks):
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2022-02-03 13:24:57 UTC (rev 694)
+++ pkg/CHNOSZ/vignettes/vig.bib 2022-02-04 04:10:05 UTC (rev 695)
@@ -1,15 +1,4 @@
- at Article{AD01,
- author = {Aksu, Serdar and Doyle, Fiona M.},
- journal = {Journal of the Electrochemical Society},
- title = {Electrochemistry of copper in aqueous glycine solutions},
- year = {2001},
- volume = {148},
- number = {1},
- pages = {B51--B57},
- doi = {10.1149/1.1344532},
-}
-
@Book{Alb03,
author = {Alberty, Robert A.},
publisher = {Wiley-Interscience},
@@ -35,12 +24,10 @@
journal = {Geology of Ore Deposits},
title = {{P}ressure-dependent stability of cadmium chloride complexes: {P}otentiometric measurements at 1-1000 bar and 25°{C}},
year = {2010},
- volume = {52},
number = {2},
pages = {167--178},
- af = {Bazarkina, E. F.EOLEOLZotov, A. V.EOLEOLAkinfiev, N. N.},
+ volume = {52},
doi = {10.1134/S1075701510020054},
- sn = {1075-7015},
}
@Book{BJH84,
@@ -49,35 +36,10 @@
title = {{E}quilibrium {A}ctivity {D}iagrams for {C}oexisting {M}inerals and {A}queous {S}olutions at {P}ressures and {T}emperatures to 5 kb and 600°{C}},
year = {1984},
address = {Heidelberg},
+ doi = {10.1007/978-3-642-46511-6},
pages = {397},
- url = {https://www.worldcat.org/oclc/11133620},
}
- at Article{DLE64,
- author = {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V.},
- journal = {Science},
- title = {{T}hermodynamic equilibria in prebiological atmospheres},
- year = {1964},
- volume = {146},
- number = {3650},
- pages = {1461--1464},
- doi = {10.1126/science.146.3650.1461},
- sn = {0036-8075},
- z8 = {0},
- z9 = {60},
- zb = {13},
-}
-
- at TechReport{DLEN67,
- author = {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. and Nagarajan, G.},
- title = {{T}hermodynamic equilibrium in prebiological atmospheres of {C}, {H}, {O}, {N}, {P}, {S}, and {C}l},
- institution = {National Aeronautics and Space Administration},
- year = {1967},
- type = {Report},
- number = {SP-3040},
- address = {Washington, D. C.},
-}
-
@Article{Dic08,
author = {Dick, Jeffrey M.},
journal = {Geochemical Transactions},
@@ -108,14 +70,6 @@
doi = {10.1098/rsif.2013.1095},
}
- at Article{Dic15,
- author = {Dick, Jeffrey M.},
- journal = {bioRxiv},
- title = {{C}hemical integration of proteins in signaling and development},
- year = {2015},
- doi = {10.1101/015826},
-}
-
@Article{DLH06,
author = {Dick, Jeffrey M. and LaRowe, Douglas E. and Helgeson, Harold C.},
journal = {Biogeosciences},
@@ -127,61 +81,17 @@
doi = {10.5194/bg-3-311-2006},
}
- at Article{DS11,
- author = {Dick, Jeffrey M. and Shock, Everett L.},
- journal = {PLOS One},
- title = {Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring},
- year = {2011},
- number = {8},
- pages = {e22782},
- volume = {6},
- doi = {10.1371/journal.pone.0022782},
-}
-
- at Article{DS13,
- author = {Dick, Jeffrey M. and Shock, Everett L.},
- journal = {PLOS One},
- title = {A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring},
- year = {2013},
- number = {9},
- pages = {e72395},
- volume = {8},
- doi = {10.1371/journal.pone.0072395},
-}
-
- at Book{GC65,
- author = {Garrels, Robert M. and Christ, Charles L.},
- publisher = {Harper \& Row},
- title = {{S}olutions, {M}inerals, and {E}quilibria},
- year = {1965},
- address = {New York},
- url = {https://www.worldcat.org/oclc/517586},
-}
-
@Article{GHB_03,
author = {Ghaemmaghami, Sina and Huh, Won-Ki and Bower, Kiowa and Howson, Russell W. and Belle, Archana and Dephoure, Noah and O'Shea, Erin K. and Weissman, Jonathan S.},
journal = {Nature},
title = {Global analysis of protein expression in yeast},
year = {2003},
- volume = {425},
number = {6959},
pages = {737--741},
+ volume = {425},
doi = {10.1038/nature02046},
}
- at InCollection{Hel70c,
- author = {Helgeson, Harold C.},
- booktitle = {Fiftieth Anniversary Symposia},
- publisher = {Mineralogical Society of America},
- title = {A chemical and thermodynamic model of ore deposition in hydrothermal systems},
- year = {1970},
- editor = {Morgan, Benjamin A.},
- pages = {155--186},
- series = {Mineralogical Society of America, Special Paper},
- volume = {3},
- url = {https://www.worldcat.org/oclc/583263},
-}
-
@Article{Hel69,
author = {Helgeson, Harold C.},
journal = {American Journal of Science},
@@ -225,15 +135,14 @@
}
@Article{HKF81,
- author = {Helgeson, Harold C. and Kirkham, David H. and Flowers, George C.},
- 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},
- number = {10},
- pages = {1249--1516},
- volume = {281},
- doi = {10.2475/ajs.281.10.1249},
- size = {268 p.},
+ author = {Helgeson, Harold C. and Kirkham, David H. and Flowers, George C.},
+ 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},
+ number = {10},
+ pages = {1249--1516},
+ volume = {281},
+ doi = {10.2475/ajs.281.10.1249},
}
@Article{JOH92,
@@ -323,19 +232,6 @@
doi = {10.2113/gsecongeo.80.7.1965},
}
- at Article{Oth76,
- author = {Othmer, H. G.},
- journal = {Chemical Engineering Science},
- title = {{N}onuniqueness of equilibria in closed reacting systems},
- year = {1976},
- volume = {31},
- number = {11},
- pages = {993--1003},
- doi = {10.1016/0009-2509(76)87020-0},
- sn = {0009-2509},
- z9 = {41},
-}
-
@Article{PS01,
author = {Plyasunov, Andrey V. and Shock, Everett L.},
journal = {Geochimica et Cosmochimica Acta},
@@ -357,26 +253,15 @@
doi = {10.1016/j.epsl.2014.11.035},
}
- at Book{Pou49,
- author = {Pourbaix, Marcel J. N.},
- publisher = {Edward Arnold \& Co.},
- title = {Thermodynamics of Dilute Aqueous Solutions},
- year = {1949},
- address = {London},
- pages = {136},
- url = {https://www.worldcat.org/oclc/1356445},
-}
-
@Article{PM90,
- author = {Privalov, P. L. and Makhatadze, G. I.},
- journal = {Journal of Molecular Biology},
- title = {Heat capacity of proteins. {II}. {P}artial molar heat capacity of the unfolded polypeptide chain of proteins: {P}rotein unfolding effects},
- year = {1990},
- volume = {213},
- number = {2},
- pages = {385--391},
- doi = {10.1016/S0022-2836(05)80198-6},
- size = {7 p.},
+ author = {Privalov, P. L. and Makhatadze, G. I.},
+ journal = {Journal of Molecular Biology},
+ title = {Heat capacity of proteins. {II}. {P}artial molar heat capacity of the unfolded polypeptide chain of proteins: {P}rotein unfolding effects},
+ year = {1990},
+ number = {2},
+ pages = {385--391},
+ volume = {213},
+ doi = {10.1016/S0022-2836(05)80198-6},
}
@Article{RH98,
@@ -401,17 +286,6 @@
pages = {461},
}
- at Article{SB01,
- 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,
author = {Schulte, Mitchell D. and Shock, Everett L.},
journal = {Origins of Life and Evolution of the Biosphere},
@@ -434,16 +308,6 @@
doi = {10.1016/S0016-7037(01)00717-7},
}
- at Article{See96,
- author = {Seewald, Jeffrey S.},
- journal = {Materials Research Society Symposium Proceedings},
- title = {{M}ineral redox buffers and the stability of organic compounds under hydrothermal conditions},
- year = {1996},
- volume = {432},
- pages = {317--331},
- doi = {10.1557/PROC-432-317},
-}
-
@Article{SC10,
author = {Shock, Everett L. and Canovas, Peter},
journal = {Geofluids},
@@ -452,35 +316,9 @@
number = {1-2},
pages = {161--192},
volume = {10},
- af = {Shock, E.EOLEOLCanovas, P.},
doi = {10.1111/j.1468-8123.2010.00277.x},
- si = {Sp. Iss. SI},
- sn = {1468-8115},
}
- at Article{Sho90b,
- author = {Shock, Everett L.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{D}o amino acids equilibrate in hydrothermal fluids?},
- year = {1990},
- volume = {54},
- number = {4},
- pages = {1185--1189},
- doi = {10.1016/0016-7037(90)90450-Y},
- issn = {0016-7037},
-}
-
- at 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},
- number = {4},
- pages = {915--945},
- volume = {54},
- doi = {10.1016/0016-7037(90)90429-O},
-}
-
@Article{SHS89,
author = {Shock, Everett L. and Helgeson, Harold C. and Sverjensky, Dimitri A.},
journal = {Geochimica et Cosmochimica Acta},
@@ -503,29 +341,6 @@
doi = {10.1039/FT9928800803},
}
- at Article{SSWS97,
- author = {Shock, Everett L. and Sassani, David C. and Willis, Marc and Sverjensky, Dimitri A.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{I}norganic species in geologic fluids: {C}orrelations among standard molal thermodynamic properties of aqueous ions and hydroxide complexes},
- year = {1997},
- number = {5},
- pages = {907--950},
- volume = {61},
- doi = {10.1016/S0016-7037(96)00339-0},
-}
-
- at Article{SS98,
- author = {Shock, Everett L. and Schulte, Mitchell D.},
- journal = {Journal of Geophysical Research},
- title = {Organic synthesis during fluid mixing in hydrothermal systems},
- year = {1998},
- number = {E12},
- pages = {28513--28527},
- volume = {103},
- doi = {10.1029/98JE02142},
- issn = {0148-0227},
-}
-
@Article{Ste01,
author = {Stefánsson, Andri},
journal = {Chemical Geology},
@@ -601,18 +416,6 @@
doi = {10.1063/1.1461829},
}
- at Article{WJD58,
- author = {White, W. B. and Johnson, S. M. and Dantzig, G. B.},
- journal = {Journal of Chemical Physics},
- title = {{C}hemical equilibrium in complex mixtures},
- year = {1958},
- volume = {28},
- number = {5},
- pages = {751--755},
- doi = {10.1063/1.1744264},
- issn = {0021-9606},
-}
-
@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},
@@ -638,11 +441,10 @@
journal = {Journal of Chemical Thermodynamics},
title = {Apparent molar heat capacities of aqueous solutions of {CH}4, {CO}2, {H}2{S}, and {NH}3 at temperatures from 304 {K} to 704 {K} at a pressure of 28 {MP}a},
year = {1997},
- volume = {29},
number = {7},
pages = {731--747},
+ volume = {29},
doi = {10.1006/jcht.1997.0192},
- issn = {0021-9614},
}
@Article{HWM96,
@@ -650,11 +452,10 @@
journal = {Journal of Chemical Thermodynamics},
title = {Volumes of aqueous solutions of {CH}4, {CO}2, {H}2{S}, and {NH}3 at temperatures from 298.15 {K} to 705 {K} and pressures to 35 {MP}a},
year = {1996},
- volume = {28},
number = {2},
pages = {125--142},
+ volume = {28},
doi = {10.1006/jcht.1996.0011},
- issn = {0021-9614},
}
@Article{AD03,
@@ -676,7 +477,6 @@
pages = {137--146},
volume = {485},
doi = {10.1016/j.jnucmat.2016.12.036},
- issn = {0022-3115},
}
@Article{MDS_13,
@@ -684,23 +484,11 @@
journal = {Nature Communications},
title = {Carbon dioxide concentration dictates alternative methanogenic pathways in oil reservoirs},
year = {2013},
+ pages = {1998},
volume = {4},
- pages = {1998},
doi = {10.1038/ncomms2998},
}
- at Article{MD98,
- author = {Merino, Enrique and Dewers, Thomas},
- journal = {Journal of Hydrology},
- title = {{I}mplications of replacement for reaction--transport modeling},
- year = {1998},
- number = {1-4},
- pages = {137--146},
- volume = {209},
- doi = {10.1016/S0022-1694(98)00150-4},
- issn = {0022-1694},
-}
-
@TechReport{Wol92,
author = {Wolery, Thomas J.},
title = {{E}q3/6, {A} {S}oftware {P}ackage for {G}eochemical {M}odeling of {A}queous {S}ystems: {P}ackage {O}verview and {I}nstallation {G}uide ({V}ersion 7.0)},
@@ -715,11 +503,10 @@
journal = {Reviews in Mineralogy and Geochemistry},
title = {{T}hermodynamic modeling of fluid-rock interaction at mid-crustal to upper-mantle conditions},
year = {2013},
- volume = {76},
number = {1},
pages = {135--164},
+ volume = {76},
doi = {10.2138/rmg.2013.76.5},
- issn = {1529-6466},
}
@Article{Ber88,
@@ -744,19 +531,14 @@
}
@Article{SVI12,
- author = {Sabatini, Antonio and Vacca, Alberto and Iotti, Stefano},
- journal = {PLoS ONE},
- title = {{B}alanced biochemical reactions: {A} new approach to unify chemical and biochemical thermodynamics},
- year = {2012},
- volume = {7},
- number = {1},
- pages = {e29529},
- doi = {10.1371/journal.pone.0029529},
- sn = {1932-6203},
- z8 = {0},
- z9 = {0},
- zb = {0},
- zs = {0},
+ author = {Sabatini, Antonio and Vacca, Alberto and Iotti, Stefano},
+ journal = {PLOS One},
+ title = {{B}alanced biochemical reactions: {A} new approach to unify chemical and biochemical thermodynamics},
+ year = {2012},
+ number = {1},
+ pages = {e29529},
+ volume = {7},
+ doi = {10.1371/journal.pone.0029529},
}
@Article{Dic19,
@@ -770,15 +552,14 @@
}
@Article{WJ17,
- author = {Thomas J. Wolery and Jov\'e Col\'on, Carlos F.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{C}hemical thermodynamic data. 1. {T}he concept of links to the chemical elements and the historical development of key thermodynamic data},
- year = {2017},
- volume = {213},
- number = {Supplement C},
- pages = {635--676},
- doi = {10.1016/j.gca.2016.09.028},
- issn = {0016-7037},
+ author = {Thomas J. Wolery and Jov\'e Col\'on, Carlos F.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{C}hemical thermodynamic data. 1. {T}he concept of links to the chemical elements and the historical development of key thermodynamic data},
+ year = {2017},
+ number = {Supplement C},
+ pages = {635--676},
+ volume = {213},
+ doi = {10.1016/j.gca.2016.09.028},
}
@TechReport{AS04,
@@ -796,12 +577,10 @@
journal = {European Journal of Biochemistry},
title = {{R}ecommendations for nomenclature and tables in biochemical thermodynamics},
year = {1996},
- volume = {240},
number = {1},
pages = {1--14},
+ volume = {240},
doi = {10.1111/j.1432-1033.1996.0001h.x},
- issn = {1432-1033},
- publisher = {Blackwell Science Ltd},
}
@Article{PAB_14,
@@ -831,12 +610,10 @@
journal = {American Mineralogist},
title = {{T}he heat capacity of {M}g{C}r$_2${O}$_4$, {F}e{C}r$_2${O}$_4$, and {C}r$_2${O}$_3$ at low temperatures and derived thermodynamic properties},
year = {2000},
- volume = {85},
number = {11-12},
pages = {1686--1693},
+ volume = {85},
doi = {10.2138/am-2000-11-1212},
- issn = {0003-004X},
- source = {Crossref},
}
@Article{PWLC12,
@@ -944,3 +721,14 @@
edition = {2nd},
url = {https://www.worldcat.org/oclc/563921897},
}
+
+ at Article{MWKL17,
+ author = {Miron, George D. and Wagner, Thomas and Kulik, Dmitrii A. and Lothenbach, Barbara},
+ journal = {American Journal of Science},
+ title = {An internally consistent thermodynamic dataset for aqueous species in the system {Ca-Mg-Na-K-Al-Si-O-H-C-Cl} to 800 °{C} and 5 kbar},
+ year = {2017},
+ number = {7},
+ pages = {755--806},
+ volume = {317},
+ doi = {10.2475/07.2017.01},
+}
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