[CHNOSZ-commits] r297 - in pkg/CHNOSZ: . R data inst inst/extdata/Berman inst/extdata/OBIGT man tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Dec 12 16:19:12 CET 2017
Author: jedick
Date: 2017-12-12 16:19:11 +0100 (Tue, 12 Dec 2017)
New Revision: 297
Added:
pkg/CHNOSZ/inst/extdata/Berman/BA96.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
pkg/CHNOSZ/man/berman.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/tests/testthat/test-berman.R
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/obigt.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
Log:
add extdata/Berman/BA96.csv (Berman and Aranovich, 1996)
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/DESCRIPTION 2017-12-12 15:19:11 UTC (rev 297)
@@ -1,6 +1,6 @@
-Date: 2017-12-05
+Date: 2017-12-12
Package: CHNOSZ
-Version: 1.1.3-3
+Version: 1.1.3-4
Title: Thermodynamic Calculations for Geobiochemistry
Authors at R: c(
person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/R/berman.R 2017-12-12 15:19:11 UTC (rev 297)
@@ -19,12 +19,13 @@
SHD91 <- read.csv(paste0(dir, "/SHD91.csv"), as.is=TRUE)
ZS92 <- read.csv(paste0(dir, "/ZS92.csv"), as.is=TRUE)
JUN92 <- read.csv(paste0(dir, "/JUN92.csv"), as.is=TRUE)
+ BA96 <- read.csv(paste0(dir, "/BA96.csv"), as.is=TRUE)
DS10 <- read.csv(paste0(dir, "/DS10.csv"), as.is=TRUE)
FDM14 <- read.csv(paste0(dir, "/FDM+14.csv"), as.is=TRUE)
BDat17 <- read.csv(paste0(dir, "/BDat17.csv"), as.is=TRUE)
# assemble the files in reverse chronological order
- dat <- rbind(BDat17, FDM14, DS10, JUN92, ZS92, SHD91, Ber90, Ber88)
- # remove duplicates (only the first, i.e. latest entry is kept)
+ dat <- rbind(BDat17, FDM14, DS10, BA96, JUN92, ZS92, SHD91, Ber90, Ber88)
+ # remove duplicates (only the first, i.e. most recent entry is kept)
dat <- dat[!duplicated(dat$name), ]
# remove the multipliers
multexp <- c(0, 0, 0, 0, # Ber88 Table 2
@@ -34,6 +35,8 @@
0, 0, 0, -3, -5, 2, 6, -4 # Table 5
)
dat[, 2:27] <- t(t(dat[, 2:27]) / 10^multexp)
+ # if name is missing, return the entire data frame (used in test-berman.R)
+ if(missing(name)) return(dat)
# which row has data for this mineral?
irow <- which(dat$name == name)
# the function works fine with just the following assign() call,
@@ -49,8 +52,8 @@
if(check.G) {
GfPrTr_calc <- HfPrTr - Tr * (SPrTr - SPrTr_elements)
Gdiff <- GfPrTr_calc - GfPrTr
- if(is.na(GfPrTr)) warning(paste0(name, ": GfPrTr(table) is NA"), call.=FALSE)
- else if(abs(Gdiff) >= 1000) warning(paste0(name, ": GfPrTr(calc) - GfPrTr(table) is too big! == ",
+ #if(is.na(GfPrTr)) warning(paste0(name, ": GfPrTr(table) is NA"), call.=FALSE)
+ if(!is.na(GfPrTr)) if(abs(Gdiff) >= 1000) warning(paste0(name, ": GfPrTr(calc) - GfPrTr(table) is too big! == ",
round(GfPrTr_calc - GfPrTr), " J/mol"), call.=FALSE)
# (the tabulated GfPrTr is unused below)
}
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/data/refs.csv 2017-12-12 15:19:11 UTC (rev 297)
@@ -49,6 +49,11 @@
SK95,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","metal-organic acid complexes",https://doi.org/10.1016/0016-7037(95)00058-8
SK95.1,"E. L. Shock and C. M. Koretsky",1995,"Geochim. Cosmochim. Acta 59, 1497-1532","alanate, glycinate and their complexes not included in later slop files.",https://doi.org/10.1016/0016-7037(95)00058-8
Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
+BA96,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","added minerals: Fe-cordierite, geikelite, hercynite, iron-a, iron-g, orthocorundum",https://doi.org/10.1007/s004100050233
+BA96.1,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and Cp + V coefficients: almandine, anthyophyllite, fayalite, ferrosilite",https://doi.org/10.1007/s004100050233
+BA96.2,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H and S: cordierite, enstatite, hematite, magnetite, rutile",https://doi.org/10.1007/s004100050233
+BA96.3,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and Cp coefficients: forsterite, pyrope, spinel",https://doi.org/10.1007/s004100050233
+BA96.4,"R. G. Berman and L. Ya. Aranovich",1996,"Contrib. Mineral. Petrol. 126, 1-24","revised H, S and V coefficients: ilmenite, talc",https://doi.org/10.1007/s004100050233
DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,http://dx.doi.org/10.1016/0016-7037(95)00403-3
AH97b,"J. P. Amend and H. C. Helgeson",1997,"J. Chem. Soc., Faraday Trans. 93, 1927-1941","amino acids GHS",https://doi.org/10.1039/A608126F
DSM+97,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024",alkylphenols,https://doi.org/10.1016/S0016-7037(97)00212-3
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/inst/NEWS 2017-12-12 15:19:11 UTC (rev 297)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-3 (2017-12-05)
+CHANGES IN CHNOSZ 1.1.3-4 (2017-12-12)
--------------------------------------
- Lines in 1-D diagram()s can optionally be drawn as splines using the
@@ -10,6 +10,9 @@
- Add 'srt' argument to diagram() (rotation of line labels).
+- Add mineral data from Berman and Aranovich, 1996 to
+ extdata/Berman/BA96.csv.
+
CHANGES IN CHNOSZ 1.1.3 (2017-11-13)
------------------------------------
Added: pkg/CHNOSZ/inst/extdata/Berman/BA96.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BA96.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/BA96.csv 2017-12-12 15:19:11 UTC (rev 297)
@@ -0,0 +1,21 @@
+name,GfPrTr,HfPrTr,SPrTr,VPrTr,k0,k1,k2,k3,v1,v2,v3,v4,Tlambda,Tref,dTdP,l1,l2,DtH,Tmax,Tmin,d0,d1,d2,d3,d4,d5
+almandine,,-5265440,341.51,11.529,621.43,-32.879,-150.81,221.187,-0.57,0.434,18.599,74.711,,,,,,,,,,,,,,
+anthophyllite,,-12074470,537.4,26.33,1233.79,-71.34,-221.638,233.394,-1.139,0,28.105,62.894,,,,,,,,,,,,,,
+cordierite,,-9161480,416.23,23.311,954.39,-79.623,-23.173,-37.021,-1.158,0,3.003,18.017,,,,,,,,,,,,,,
+Fe-cordierite,,-8430550,482.18,23.706,983.48,-84.037,-18.703,-8.568,-1.7,0,4.265,0,,,,,,,,,,,,,,
+fayalite,,-1477170,151.73,4.639,252,-20.137,0,-6.219,-0.822,1.944,26.21,84.233,,,,,,,,,,,,,,
+ferrosilite,,-1192910,96.47,3.295,174.2,-13.93,-4.544,-3.771,-0.911,0.303,31.406,80.4,,,,,,,,,,,,,,
+forsterite,,-2174420,94.18,4.36,233.18,-18.016,0,-26.794,-0.791,1.351,29.464,88.633,,,,,,,,,,,,,,
+geikelite,,-1570520,74.41,3.077,146.2,-4.16,-39.998,40.233,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
+hematite,,-826740,87.36,3.027,146.86,0,-55.768,52.563,-0.479,0.304,38.31,1.65,955,298,0,-7.403,27.921,1287,,,,,,,,
+hercynite,,-1945360,123.13,4.08,251.77,-20.444,-13.483,13.15,-0.51,0,15.819,96.276,,,,,,,,,,,,,,
+ilmenite,,-1233320,108.5,3.17,150,-4.416,-33.237,34.815,-0.529,0,23.314,88.328,,,,,,,,,,,,,,
+iron-a,,0,27.45,0.709,51.87,-3.794,-25.43,50.68,-0.602,0,45.071,14.104,1042,298,-0.00057,-22.208,34.823,1000,,,,,,,,
+iron-g,,7720,35.64,0.691,66.24,-12.371,63.733,-106.04,-0.467,-1.445,47.153,14.451,,,,,,,,,,,,,,
+magnetite,,-1116960,146.04,4.452,207.93,0,-72.433,66.436,-0.582,1.751,30.291,138.47,848,298,0,-19.502,61.037,1565,,,,,,,,
+enstatite,,-1546040,66.18,3.133,166.58,-12.006,-22.706,27.915,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
+orthocorundum,,-1634950,33.93,3.123,119.38,7.748,-65.091,42.288,-0.749,0.447,24.656,74.67,,,,,,,,,,,,,,
+pyrope,,-6284740,268.8,11.311,590.9,-28.27,-133.208,126.033,-0.576,0.442,22.519,37.044,,,,,,,,,,,,,,
+rutile,,-944750,50.88,1.883,77.84,0,-33.678,40.294,-0.454,0.585,25.716,15.409,,,,,,,,,,,,,,
+spinel,,-2302160,80.37,3.978,244.67,-20.04,,,-0.489,0,21.691,50.528,,,,,,,,,,,,,,
+talc,,-5898960,261.21,13.61,664.11,-51.872,-21.472,-32.737,-1.847,5.878,25.616,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/man/berman.Rd
===================================================================
--- pkg/CHNOSZ/man/berman.Rd 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/man/berman.Rd 2017-12-12 15:19:11 UTC (rev 297)
@@ -24,12 +24,13 @@
\details{
This function calculates the thermodynamic properties of minerals at high \P and \T using equations given by Berman (1988).
-The \code{name} refers to a mineral that must be listed in \code{thermo$obigt} with the state \samp{cr_Berman}.
-This file also holds the chemical formula, which is required for calculating the entropies of the elements in the mineral.
+Becuase they use a different set of parameters than Helgeson et al., 1978 (see \code{\link{cgl}}), the standard state thermodynamic properties and parameters for the calculations are stored in files under \code{extdata/Berman}.
+If the function is called with missing \code{name}, the data frame of parameters for all available minerals is returned.
+
+When \code{name} is given, it refers to a mineral that should listed in \code{thermo$obigt} with the state \samp{cr_Berman}.
+\code{thermo$obigt} also holds the chemical formula, which is required for calculating the entropies of the elements in the mineral.
These entropies are used to convert the apparent Gibbs energies from the Berman-Brown convention to the the Benson-Helgeson convention (cf. Anderson, 2005).
-Becuase they use a different set of parameters than Helgeson et al., 1978 (see \code{\link{cgl}}), the standard state thermodynamic properties and parameters for the calculations are stored in files under \code{extdata/Berman}.
-
If \code{check.G} is TRUE, the tabulated value of DGfTrPr is compared with one calculated from DHfPrTr - T*DSPrTr (DS is the difference between the summed entropies of the elements and the tabulated entropy for the mineral).
A warning is produced if the absolute value of the difference between tabulated and calculated DGfTrPr is greater than 1000 J/mol.
Modified: pkg/CHNOSZ/man/examples.Rd
===================================================================
--- pkg/CHNOSZ/man/examples.Rd 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/man/examples.Rd 2017-12-12 15:19:11 UTC (rev 297)
@@ -23,7 +23,7 @@
\details{
-\code{examples} runs all the examples in the documentation for the package.
+\code{examples} runs all the examples in the help pages for the package.
\code{\link{example}} is called for each topic with \code{ask} set to \code{FALSE} (so all of the figures are shown without prompting the user).
\code{demos} runs all the \code{\link{demo}s} in the package.
Modified: pkg/CHNOSZ/tests/testthat/test-berman.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-berman.R 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/tests/testthat/test-berman.R 2017-12-12 15:19:11 UTC (rev 297)
@@ -1,26 +1,15 @@
# test-berman.R 20171001
context("berman")
-# calculate properties for all available minerals at Tr,Pr
-dir <- system.file("extdata/Berman/", package="CHNOSZ")
-Ber88 <- read.csv(paste0(dir, "/Ber88.csv"), as.is=TRUE)
-Ber90 <- read.csv(paste0(dir, "/Ber90.csv"), as.is=TRUE)
-SHD91 <- read.csv(paste0(dir, "/SHD91.csv"), as.is=TRUE)
-ZS92 <- read.csv(paste0(dir, "/ZS92.csv"), as.is=TRUE)
-JUN92 <- read.csv(paste0(dir, "/JUN92.csv"), as.is=TRUE)
-DS10 <- read.csv(paste0(dir, "/DS10.csv"), as.is=TRUE)
-FDM14 <- read.csv(paste0(dir, "/FDM+14.csv"), as.is=TRUE)
-BDat17 <- read.csv(paste0(dir, "/BDat17.csv"), as.is=TRUE)
-# assemble the files and remove duplicates (keep the latest)
-dat <- rbind(BDat17, FDM14, DS10, ZS92, SHD91, Ber90, Ber88)
-dat <- dat[!duplicated(dat$name), ]
+# get parameters for all available minerals
+dat <- berman()
mineral <- unique(dat$name)
prop_Berman <- NULL
test_that("properties of all minerals are computed without warnings", {
# running this without error means that:
# - formulas for the minerals are found in thermo$obigt
- # - warnings are produced for mineral(s) with GfPrTr(calc) >= 1000 J/cal different from GfPrTr(table)
+ # - warning is produced for flourtremolite (GfPrTr(calc) >= 1000 J/cal different from GfPrTr(table))
expect_warning(properties <- lapply(mineral, berman, check.G=TRUE),
"fluortremolite", all=TRUE)
# save the results so we can use them in the next tests
@@ -43,13 +32,13 @@
# which minerals differ in DGf by more than 4 kcal/mol?
idiffG <- which(abs(prop_Berman$G - prop_Helgeson$G) > 4000)
expect_match(mineral[idiffG],
- "paragonite|anthophyllite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite")
+ "paragonite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite")
# which minerals differ in DHf by more than 4 kcal/mol?
idiffH <- which(abs(prop_Berman$H - prop_Helgeson$H) > 4000)
# we get the above, plus phlogopite and clinozoisite:
expect_match(mineral[idiffH],
- "paragonite|anthophyllite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite|phlogopite|clinozoisite")
+ "paragonite|antigorite|Ca-Al-pyroxene|lawsonite|margarite|merwinite|clinozoisite")
# which minerals differ in S by more than 4 cal/K/mol?
idiffS <- which(abs(prop_Berman$S - prop_Helgeson$S) > 4)
@@ -57,7 +46,7 @@
# which minerals differ in Cp by more than 4 cal/K/mol?
idiffCp <- which(abs(prop_Berman$Cp - prop_Helgeson$Cp) > 4)
- expect_match(mineral[idiffCp], "glaucophane|antigorite|cristobalite,beta|K-feldspar|fluortremolite|grunerite")
+ expect_match(mineral[idiffCp], "glaucophane|antigorite|cristobalite,beta|K-feldspar|fluortremolite|grunerite|almandine")
# which minerals differ in V by more than 1 cm^3/mol?
idiffV <- which(abs(prop_Berman$V - prop_Helgeson$V) > 1)
Modified: pkg/CHNOSZ/vignettes/anintro.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/anintro.Rmd 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/vignettes/anintro.Rmd 2017-12-12 15:19:11 UTC (rev 297)
@@ -2149,10 +2149,6 @@
Thank you for reading, and have fun!
-> "As any practitioner knows, the effort of research is so tedious and time consuming that when the work stops being fun, there's no sense in continuing. The best scientists live a life of keen amusement."
->
-> `r tufte::quote_footer('--- Stephen Jay Gould')`
-
> "The real fun of life is this perpetual testing to realize how far out you can go with any potentialities."
>
> `r tufte::quote_footer('--- Richard P. Feynman')`
Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd 2017-12-12 15:19:11 UTC (rev 297)
@@ -103,9 +103,9 @@
```
This [vignette](index.html), produced on `r Sys.Date()`, documents the sources of thermodynamic data in CHNOSZ version `r sessionInfo()$otherPkgs$CHNOSZ$Version`.
-Running `data(thermo)` creates the default database (`thermo$obigt`) in the R session.
+Running <span style='color:red'>`data(thermo)`</span> creates the default database (`thermo$obigt`) in the R session.
-The sections below correspond to CSV data files that are stored in the `extdata/OBIGT` package directory and read by `data(thermo)` (except for Optional Data).
+The sections below correspond to CSV data files that are stored in the `extdata/OBIGT` package directory and read by <span style='color:red'>`data(thermo)`</span> (except for Optional Data).
In each section, the primary references (`ref1` in `thermo$obigt`) are listed in chronological order.
Any secondary references (`ref2`) are listed with bullet points.
Each reference is followed by the number of species, and a note (from `thermo$refs`).
Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib 2017-12-05 03:18:53 UTC (rev 296)
+++ pkg/CHNOSZ/vignettes/obigt.bib 2017-12-12 15:19:11 UTC (rev 297)
@@ -120,24 +120,24 @@
}
@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},
+ volume = {3},
+ number = {3},
+ pages = {311--336},
+ doi = {10.5194/bg-3-311-2006},
}
@Book{HGK84,
- author = {Haar, Lester and Gallagher, John S. and Kell, George S.},
- publisher = {Hemisphere Publishing Corporation},
- title = {{NBS}/{NRC} {S}team {T}ables: {T}hermodynamic and {T}ransport {P}roperties and {C}omputer {P}rograms for {V}apor and {L}iquid {S}tates of {W}ater in {SI} {U}nits},
- year = {1984},
- address = {Washington, D. C.},
- pages = {320},
- url = {http://www.worldcat.org/oclc/858456124},
+ author = {Haar, Lester and Gallagher, John S. and Kell, George S.},
+ publisher = {Hemisphere Publishing Corporation},
+ title = {{NBS}/{NRC} {S}team {T}ables: {T}hermodynamic and {T}ransport {P}roperties and {C}omputer {P}rograms for {V}apor and {L}iquid {S}tates of {W}ater in {SI} {U}nits},
+ year = {1984},
+ address = {Washington, D. C.},
+ pages = {320},
+ url = {http://www.worldcat.org/oclc/858456124},
}
@Article{HSS95,
@@ -219,14 +219,14 @@
}
@Article{JOH92,
- author = {Johnson, James W. and Oelkers, Eric H. and Helgeson, Harold C.},
- 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},
- doi = {10.1016/0098-3004(92)90029-Q},
+ author = {Johnson, James W. and Oelkers, Eric H. and Helgeson, Harold C.},
+ 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},
+ doi = {10.1016/0098-3004(92)90029-Q},
}
@Book{Kel60,
@@ -250,25 +250,25 @@
}
@Article{LH06a,
- author = {LaRowe, Douglas E. and Helgeson, Harold C.},
- journal = {Geochimica et Cosmochimica Acta},
- title = {{B}iomolecules in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures},
- year = {2006},
- volume = {70},
- number = {18},
- pages = {4680--4724},
- doi = {10.1016/j.gca.2006.04.010},
+ author = {LaRowe, Douglas E. and Helgeson, Harold C.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{B}iomolecules in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of nucleic-acid bases, nucleosides, and nucleotides at elevated temperatures and pressures},
+ year = {2006},
+ volume = {70},
+ number = {18},
+ pages = {4680--4724},
+ doi = {10.1016/j.gca.2006.04.010},
}
@Article{LH06b,
- author = {LaRowe, Douglas E. and Helgeson, Harold C.},
- journal = {Thermochimica Acta},
- title = {{T}he energetics of metabolism in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of magnesium-complexed adenosine nucleotides and {NAD} and {NADP} at elevated temperatures and pressures},
- year = {2006},
- volume = {448},
- number = {2},
- pages = {82--106},
- doi = {10.1016/j.tca.2006.06.008},
+ author = {LaRowe, Douglas E. and Helgeson, Harold C.},
+ journal = {Thermochimica Acta},
+ title = {{T}he energetics of metabolism in hydrothermal systems: {C}alculation of the standard molal thermodynamic properties of magnesium-complexed adenosine nucleotides and {NAD} and {NADP} at elevated temperatures and pressures},
+ year = {2006},
+ volume = {448},
+ number = {2},
+ pages = {82--106},
+ doi = {10.1016/j.tca.2006.06.008},
}
@Article{MGN03,
@@ -631,14 +631,14 @@
}
@Article{SH88,
- 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: {C}orrelation algorithms for ionic species and equation of state predictions to 5 kb and 1000$^\circ${C}},
- year = {1988},
- volume = {52},
- number = {8},
- pages = {2009--2036},
- doi = {10.1016/0016-7037(88)90181-0},
+ author = {Shock, Everett L. and Helgeson, Harold C.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {C}orrelation algorithms for ionic species and equation of state predictions to 5 kb and 1000$^\circ${C}},
+ year = {1988},
+ volume = {52},
+ number = {8},
+ pages = {2009--2036},
+ doi = {10.1016/0016-7037(88)90181-0},
}
@Article{SH90,
@@ -775,14 +775,14 @@
}
@Article{TH88,
- author = {Tanger, IV, John C. and Helgeson, Harold C.},
- journal = {American Journal of Science},
- title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {R}evised equations of state for the standard partial molal properties of ions and electrolytes},
- year = {1988},
- volume = {288},
- number = {1},
- pages = {19--98},
- doi = {10.2475/ajs.288.1.19},
+ author = {Tanger, IV, John C. and Helgeson, Harold C.},
+ journal = {American Journal of Science},
+ title = {{C}alculation of the thermodynamic and transport properties of aqueous species at high pressures and temperatures: {R}evised equations of state for the standard partial molal properties of ions and electrolytes},
+ year = {1988},
+ volume = {288},
+ number = {1},
+ pages = {19--98},
+ doi = {10.2475/ajs.288.1.19},
}
@Article{TSD97,
@@ -1225,3 +1225,16 @@
url = {http://www.ingentaconnect.com/content/10.1127/0935-1221/2010/0022-2021},
}
+ at Article{BA96,
+ author = {Berman, R. G. and Aranovich, L. {\relax Ya}.},
+ journal = {Contributions to Mineralogy and Petrology},
+ title = {{O}ptimized standard state and solution properties of minerals. {I}. {M}odel calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system {F}e{O}-{M}g{O}-{C}a{O}-{A}l$_2${O}$_3$-{T}i{O}$_2$-{S}i{O}$2$},
+ year = {1996},
+ volume = {126},
+ number = {1},
+ pages = {25--37},
+ day = {01},
+ doi = {10.1007/s004100050233},
+ issn = {1432-0967},
+}
+
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