[CHNOSZ-commits] r858 - in pkg/CHNOSZ: . R demo inst inst/extdata inst/extdata/OBIGT inst/extdata/OBIGT/testing man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Dec 25 04:04:02 CET 2024
Author: jedick
Date: 2024-12-25 04:04:01 +0100 (Wed, 25 Dec 2024)
New Revision: 858
Added:
pkg/CHNOSZ/demo/references.R
pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM.csv
pkg/CHNOSZ/inst/extdata/OBIGT/testing/Sandia.csv
pkg/CHNOSZ/inst/extdata/OBIGT/testing/SiO2.csv
pkg/CHNOSZ/inst/extdata/refs.csv
Removed:
pkg/CHNOSZ/demo/sources.R
pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
pkg/CHNOSZ/inst/extdata/OBIGT/testing/AS04.csv
pkg/CHNOSZ/inst/extdata/OBIGT/testing/IGEM24.csv
pkg/CHNOSZ/inst/extdata/OBIGT/testing/KBJ24.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/add.OBIGT.R
pkg/CHNOSZ/R/examples.R
pkg/CHNOSZ/R/thermo.R
pkg/CHNOSZ/demo/00Index
pkg/CHNOSZ/demo/aluminum.R
pkg/CHNOSZ/inst/CHECKLIST
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/man/add.OBIGT.Rd
pkg/CHNOSZ/man/examples.Rd
pkg/CHNOSZ/vignettes/OBIGT.Rmd
pkg/CHNOSZ/vignettes/anintro.Rmd
pkg/CHNOSZ/vignettes/custom_data.Rmd
pkg/CHNOSZ/vignettes/eos-regress.Rmd
Log:
Rename some files in OBIGT/testing
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/DESCRIPTION 2024-12-25 03:04:01 UTC (rev 858)
@@ -1,6 +1,6 @@
-Date: 2024-12-24
+Date: 2024-12-25
Package: CHNOSZ
-Version: 2.1.0-30
+Version: 2.1.0-31
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/add.OBIGT.R
===================================================================
--- pkg/CHNOSZ/R/add.OBIGT.R 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/R/add.OBIGT.R 2024-12-25 03:04:01 UTC (rev 858)
@@ -120,8 +120,8 @@
if(!file.exists(file)) {
# List all files in OBIGT and OBIGT/testing
- OBIGT_files <- dir(system.file("extdata/OBIGT/", package = "CHNOSZ"), full.names = TRUE)
- testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), full.names = TRUE)
+ OBIGT_files <- dir(system.file("extdata/OBIGT", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
+ testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
all_files <- c(OBIGT_files, testing_files)
# Match argument to file names without path or .csv suffix
all_names <- gsub(".csv", "", basename(all_files))
Modified: pkg/CHNOSZ/R/examples.R
===================================================================
--- pkg/CHNOSZ/R/examples.R 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/R/examples.R 2024-12-25 03:04:01 UTC (rev 858)
@@ -30,7 +30,7 @@
cat("Time elapsed: ", proc.time() - .ptime, "\n")
}
-demos <- function(which = c("sources", "protein.equil", "affinity", "NaCl", "density",
+demos <- function(which = c("references", "protein.equil", "affinity", "NaCl", "density",
"ORP", "ionize", "buffer", "protbuff", "glycinate",
"mosaic", "copper", "arsenic", "solubility", "gold", "contour", "sphalerite", "minsol",
"Shh", "saturation", "adenine", "DEW", "lambda", "potassium", "TCA", "aluminum",
Modified: pkg/CHNOSZ/R/thermo.R
===================================================================
--- pkg/CHNOSZ/R/thermo.R 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/R/thermo.R 2024-12-25 03:04:01 UTC (rev 858)
@@ -78,7 +78,7 @@
# Create OBIGT data frame
OBIGT <- do.call(rbind, datalist)
# Also read references file
- refs <- read.csv(file.path(OBIGTdir, "refs.csv"), as.is = TRUE)
+ refs <- read.csv(file.path(OBIGTdir, "../refs.csv"), as.is = TRUE)
# Get thermo from CHNOSZ environment
thermo <- get("thermo", CHNOSZ)
# Set OBIGT and refs
Modified: pkg/CHNOSZ/demo/00Index
===================================================================
--- pkg/CHNOSZ/demo/00Index 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/demo/00Index 2024-12-25 03:04:01 UTC (rev 858)
@@ -1,4 +1,4 @@
-sources Cross-check the reference list with the thermodynamic database
+references Cross-check the references in refs.csv with the thermodynamic database
protein.equil Chemical activities of two proteins in metastable equilibrium
affinity Affinities of metabolic reactions and amino acid synthesis
NaCl Equilibrium constant for aqueous NaCl dissociation
Modified: pkg/CHNOSZ/demo/aluminum.R
===================================================================
--- pkg/CHNOSZ/demo/aluminum.R 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/demo/aluminum.R 2024-12-25 03:04:01 UTC (rev 858)
@@ -25,7 +25,7 @@
# boehmite from Hemingway et al., 1991
r1 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
## Second calculation: get SiO2(aq) from Apps and Spycher, 2004
-add.OBIGT("AS04")
+add.OBIGT("SiO2")
r2 <- subcrt(c("boehmite", "H2O", "SiO2", "kaolinite"), c(-1, -0.5, -1, 0.5), T = T, P = 1000, exceed.Ttr = TRUE)
reset()
## Third calculation: get Si(OH)4 from Akinfiev and Plyasunov, 2014
@@ -48,7 +48,7 @@
title(main = describe.reaction(r4$reaction), cex.main = 1.1)
legend("bottomright", lty = c(0, 0, 1, 2, 3, 0), pch = c(1, 4, NA, NA, NA, NA), lwd = c(1, 1, 1.5, 1, 1, 0),
col = c("black", "red", "black", "red", "purple", NA), bty = "n", cex = 0.9,
- legend = c("Hemley et al., 1980", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("AS04")', 'add.OBIGT("AD")', ""))
+ legend = c("Hemley et al., 1980", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("SiO2")', 'add.OBIGT("AD")', ""))
legend("bottomright", lty = 4, pch = NA, lwd = 1, col = "blue", legend = 'add.OBIGT("SUPCRT92")', bty = "n", cex = 0.9)
legend("topleft", c("Boehmite - Kaolinite", "After Zhu and Lu, 2009 Fig. A1"), bty = "n")
# Helgeson et al., 1978 (HDNB78): http://www.worldcat.org/oclc/13594862
@@ -105,7 +105,7 @@
pK <- -sres$out$logK
lines(invTK, pK, lwd = 1.5)
# Plot line: SiO2 from Apps and Spycher, 2004
-add.OBIGT("AS04")
+add.OBIGT("SiO2")
sres <- subcrt(c("kaolinite", "OH-", "H2O", "Al(OH)4-", "SiO2"), c(-1, -2, -1, 2, 2), T = T)
pK <- -sres$out$logK
lines(invTK, pK, col = "red", lty = 2)
@@ -133,7 +133,7 @@
legend("topright", c("Kaolinite solubility", "After Tutolo et al., 2014 Fig. 2"), bty = "n")
legend("bottomleft", lty = c(0, 0, 0, 1, 2, 3, 4), pch = c(1, NA, 4, NA, NA, NA, NA),
lwd = c(1, 1, 1, 1.5, 1, 1, 1), col = c("black", "black", "red", "black", "red", "purple", "blue"),
- legend = c("Various sources \u2013", " see Tutolo et al., 2014", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("AS04")', 'add.OBIGT("AD")', 'add.OBIGT("SUPCRT92")'),
+ legend = c("Various sources \u2013", " see Tutolo et al., 2014", "SUPCRTBL", "CHNOSZ", 'add.OBIGT("SiO2")', 'add.OBIGT("AD")', 'add.OBIGT("SUPCRT92")'),
bty = "n", cex = 0.9)
###########
Copied: pkg/CHNOSZ/demo/references.R (from rev 857, pkg/CHNOSZ/demo/sources.R)
===================================================================
--- pkg/CHNOSZ/demo/references.R (rev 0)
+++ pkg/CHNOSZ/demo/references.R 2024-12-25 03:04:01 UTC (rev 858)
@@ -0,0 +1,36 @@
+# CHNOSZ/demo/reference.R
+## Cross-checking references
+library(CHNOSZ)
+
+# The available reference keys
+available_refs <- thermo()$refs$key
+
+# The used reference keys
+# List all files in OBIGT and OBIGT/testing
+OBIGT_files <- dir(system.file("extdata/OBIGT", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
+testing_files <- dir(system.file("extdata/OBIGT/testing", package = "CHNOSZ"), pattern = ".csv", full.names = TRUE)
+all_files <- c(OBIGT_files, testing_files)
+all_data <- lapply(all_files, read.csv)
+all_data <- do.call(rbind, all_data)
+used_refs <- na.omit(c(all_data$ref1, all_data$ref2))
+
+# Print messages for unavailable and unused refs
+unavailable_refs <- used_refs[!used_refs %in% available_refs]
+unused_refs <- available_refs[!available_refs %in% used_refs]
+if(length(unavailable_refs) > 0 | length(unused_refs) > 0) {
+
+ if(length(unavailable_refs) > 0) {
+ print("References used in database but not available in refs.csv:")
+ print(unique(unavailable_refs))
+ }
+
+ if(length(unused_refs) > 0) {
+ print("References available in refs.csv but not used in database:")
+ print(unique(unused_refs))
+ }
+
+} else {
+
+ print("All references accounted for!")
+
+}
Deleted: pkg/CHNOSZ/demo/sources.R
===================================================================
--- pkg/CHNOSZ/demo/sources.R 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/demo/sources.R 2024-12-25 03:04:01 UTC (rev 858)
@@ -1,40 +0,0 @@
-# CHNOSZ/demo/sources.R
-## Cross-checking sources
-library(CHNOSZ)
-
-# The reference sources
-ref.source <- thermo()$refs$key
-# Sources in the primary thermodynamic database
-# Se omit the [S92] in "HDNB78 [S92]" etc.
-tdata <- thermo()$OBIGT
-ps1 <- gsub("\ .*", "", tdata$ref1)
-ps2 <- gsub("\ .*", "", tdata$ref2)
-# Sources in the optional datafiles
-tdata <- read.csv(system.file("extdata/OBIGT/DEW.csv", package="CHNOSZ"), as.is=TRUE)
-os1 <- gsub("\ .*", "", tdata$ref1)
-os2 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/SLOP98.csv", package="CHNOSZ"), as.is=TRUE)
-os3 <- gsub("\ .*", "", tdata$ref1)
-os4 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/SUPCRT92.csv", package="CHNOSZ"), as.is=TRUE)
-os5 <- gsub("\ .*", "", tdata$ref1)
-os6 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/AS04.csv", package="CHNOSZ"), as.is=TRUE)
-os7 <- gsub("\ .*", "", tdata$ref1)
-os8 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/AD.csv", package="CHNOSZ"), as.is=TRUE)
-os9 <- gsub("\ .*", "", tdata$ref1)
-os10 <- gsub("\ .*", "", tdata$ref2)
-tdata <- read.csv(system.file("extdata/OBIGT/GEMSFIT.csv", package="CHNOSZ"), as.is=TRUE)
-os11 <- gsub("\ .*", "", tdata$ref1)
-os12 <- gsub("\ .*", "", tdata$ref2)
-# All of the thermodynamic data sources - some of them might be NA
-OBIGT.source <- unique(c(ps1, ps2, os1, os2, os3, os4, os5, os6, os7, os8, os9, os10, os11, os12))
-OBIGT.source <- OBIGT.source[!is.na(OBIGT.source)]
-# These all produce character(0) if the sources are all accounted for
-print("missing these sources for thermodynamic properties:")
-print(unique(OBIGT.source[!(OBIGT.source %in% ref.source)]))
-# Determine if all the reference sources are cited
-# This should produce character(0)
-print("these sources are present but not cited:")
-print(ref.source[!(ref.source %in% OBIGT.source)])
Modified: pkg/CHNOSZ/inst/CHECKLIST
===================================================================
--- pkg/CHNOSZ/inst/CHECKLIST 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/inst/CHECKLIST 2024-12-25 03:04:01 UTC (rev 858)
@@ -1,6 +1,6 @@
****************************
Release checklist for CHNOSZ
- (updated 2024-02-11)
+ (updated 2024-12-25)
****************************
- Run examples() and demos() and inspect their output (especially plots)
@@ -19,11 +19,11 @@
- Add BibTeX references to vignettes/OBIGT.bib
(used in the OBIGT.Rmd vignette).
-- Add references and notes to extdata/OBIGT/refs.csv
+- Add references and notes to extdata/refs.csv
(also used in the OBIGT.Rmd vignette and thermo.refs()).
-- Check output of demo/sources.R to make sure all references
- are cited (printed results should be character(0)).
+- Check output of demo/references.R to cross-check references in refs.csv with
+ OBIGT files.
- Rebuild extdata/thermo/stoich.csv.xz after all data updates
(used in retrieve() to search the databse by element):
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2024-12-25 03:04:01 UTC (rev 858)
@@ -52,13 +52,13 @@
have been moved to \file{SLOP98.csv}.
\item Make new directory \file{OBIGT/testing} to hold optional data files
- for testing (currently \file{AS04.csv}, \file{GEMSFIT.csv},
- \file{IGEM24.csv}, and \file{KBJ24.csv}).
+ for testing (currently \file{SiO2.csv}, \file{GEMSFIT.csv},
+ \file{IGEM.csv}, and \file{Sandia.csv}).
- \item Add \file{IGEM24.csv}: updated data for Au and Cu complexes and
+ \item Add \file{IGEM.csv}: updated data for Au and Cu complexes and
SO\s{4}\S{-2}-bearing species from researchers at IGEM RAS.
- \item Add \file{KBJ24.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
+ \item Add \file{Sandia.csv}: Mg(OH)\s{2}-MgCl\s{2}-H\s{2}O phases from
\href{https://doi.org/10.1016/j.apgeochem.2024.106032}{Knight et al.
(2024)}.
Deleted: pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-12-25 02:21:18 UTC (rev 857)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/refs.csv 2024-12-25 03:04:01 UTC (rev 858)
@@ -1,303 +0,0 @@
-key,author,year,citation,note,URL
-Kel60,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gases Cp",https://www.worldcat.org/oclc/693388901
-Kel60.2,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","iron Cp",https://www.worldcat.org/oclc/693388901
-Kel60.3,"K. K. Kelley",1960,"U. S. Bureau of Mines Bull. 584","gypsum Cp",https://www.worldcat.org/oclc/693388901
-Pan70,"L. B. Pankratz",1970,"U. S. Bureau of Mines Report of Investigations 7430",chlorargyrite,https://www.worldcat.org/oclc/14154245
-PK70,"L. B. Pankratz and E. G. King",1970,"U. S. Bureau of Mines Report of Investigations 7435","bornite and chalcopyrite",https://www.worldcat.org/oclc/14154292
-RH72,"R. A. Robie and B. S. Hemingway",1972,"Am. Mineral. 57, 1768-1781","nesquehonite Cp",https://pubs.geoscienceworld.org/msa/ammin/article-pdf/57/11-12/1768/4256711/am-1972-1768.pdf
-BKK77,"I. Barin, O. Knacke and O. Kubaschewski",1977,"Thermochemical Properties of Inorganic Substances: Supplement","willemite Cp",https://www.worldcat.org/oclc/695258
-HDNB78,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229",minerals,https://www.worldcat.org/oclc/13594862
-HDNB78.2,"H. C. Helgeson, J. M. Delany et al.",1978,"Am. J. Sci. 278A, 1-229","celestite V and Cp parameters",https://www.worldcat.org/oclc/13594862
-RHF78,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",chlorargyrite,https://doi.org/10.3133/b1452
-RHF78.2,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452",iron,https://doi.org/10.3133/b1452
-RHF78.3,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","gibbsite GHS",https://doi.org/10.3133/b1452
-RHF78.4,"R. A. Robie, B. S. Hemingway and J. R. Fisher",1978,"U. S. Geological Survey Bull. 1452","rutile and titanite",https://doi.org/10.3133/b1452
-PB82,"L. N. Plummer and E. Busenberg",1982,"Geochim. Cosmochim. Acta 46, 1011-1040","aragonite and calcite",https://doi.org/10.1016/0016-7037(82)90056-4
-WEP+82,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","gases GHS",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
-WEP+82.1,"D. D. Wagman, W. H. Evans et al.",1982,"J. Phys. Chem. Ref. Data 11, Suppl. 2, 1-392","Mn(OH)<sub>2</sub> (amorphous) and MgSO<sub>4</sub>",https://srd.nist.gov/JPCRD/jpcrdS2Vol11.pdf
-BH83,"T. S. Bowers and H. C. Helgeson",1983,"Geochim. Cosmochim. Acta 47, 1247-1275",rutile,https://doi.org/10.1016/0016-7037(83)90066-2
-HGK84,"L. Haar and J. S. Gallagher and G. S. Kell",1984,"NBS/NRC Steam Tables",H<sub>2</sub>O,https://www.worldcat.org/oclc/858456124
-Hel85,"H. C. Helgeson",1985,"Am. J. Sci. 285, 845-855","ferrosilite and siderite",https://doi.org/10.2475/ajs.285.9.845
-JH85,"K. J. Jackson and H. C. Helgeson",1985,"Econ. Geol. 80, 1365-1378","Sn minerals",https://doi.org/10.2113/gsecongeo.80.5.1365
-PMW87,"L. B. Pankratz, A. D. Mah and S. W. Watson",1987,"Thermodynamic Properties of Sulfides (U.S. Bureau of Mines Bull. 689)","cattierite, linnaeite, and Co-pentlandite",https://www.worldcat.org/oclc/16131757
-RA87,"E. J. Reardon and D. K. Armstrong",1987,"Geochim. Cosmochim. Acta 51, 63-72","celestite GHS",https://doi.org/10.1016/0016-7037(87)90007-X
-RS87,"J. R. Ruaya and T. M. Seward",1987,"Geochim. Cosmochim. Acta 51, 121-130",HCl,https://doi.org/10.1016/0016-7037(87)90013-5
-Ber88,"R. G. Berman",1988,"J. Petrol. 29, 445-522",minerals,https://doi.org/10.1093/petrology/29.2.445
-OH88,"E. H. Oelkers and H. C. Helgeson",1988,"J. Phys. Chem. 92, 1631-1639",KCl,https://doi.org/10.1016/0016-7037(88)90181-0
-SH88,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","ionic species",https://doi.org/10.1016/0016-7037(88)90181-0
-SH88.1,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","values of GHS",https://doi.org/10.1016/0016-7037(88)90181-0
-SH88.2,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",H<sub>2</sub>AsO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
-SH88.3,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036",Ag<sup>+</sup>,https://doi.org/10.1016/0016-7037(88)90181-0
-SH88.4,"E. L. Shock and H. C. Helgeson",1988,"Geochim. Cosmochim. Acta 52, 2009-2036","K<sup>+</sup>, Na<sup>+</sup>, Ca<sup>+2</sup>, Mg<sup>+2</sup>, Cl<sup>-</sup>, and OH<sup>-</sup>",https://doi.org/10.1016/0016-7037(88)90181-0
-SHS89,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183","inorganic neutral species",https://doi.org/10.1016/0016-7037(89)90341-4
-SHS89.1,"E. L. Shock, H. C. Helgeson and D. A. Sverjensky",1989,"Geochim. Cosmochim. Acta 53, 2157-2183",SiO<sub>2</sub>,https://doi.org/10.1016/0016-7037(89)90341-4
-Ber90,"R. G. Berman",1990,"Am. Mineral. 75, 328-344",annite,http://ammin.geoscienceworld.org/content/75/3-4/328
-Ber90.1,"R. G. Berman",1990,"Am. Mineral. 75, 328-344","almandine and ilmenite: modified H and/or S",http://ammin.geoscienceworld.org/content/75/3-4/328
-Eva90,"B. W. Evans",1990,"Lithos 25, 3-23","glaucophane and pumpellyite",https://doi.org/10.1016/0024-4937(90)90003-J
-Pol90,"D. A. Polya",1990,"Trans. Inst. Min. Metall. 99, B120-B124","ferberite G, S and Cp (Cp coefficients multiplied by 4.184 to convert to J, as listed in @WS00, but who give a 2nd term that is off by a factor of 10). Cp at 25 °C is from @LW74.",
-OH90,"E. H. Oelkers and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 727-738","Debye-Hückel extended term parameter (<i>b</i><sub>$\gamma$</sub>)",https://doi.org/10.1016/0016-7037(90)90368-U
-SH90,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","organic species",https://doi.org/10.1016/0016-7037(90)90429-O
-HRA91,"B. S. Hemingway et al.",1991,"Am. Mineral. 76, 445-457",boehmite,https://pubs.usgs.gov/publication/70016664
-SHD91,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","G and H revisions for K- and Al-bearing silicates",https://doi.org/10.1016/0016-7037(89)90341-4
-SHD91.1,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","phlogopite: H and S modified by @Ber90, followed by G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
-SHD91.2,"D. A. Sverjensky, J. J. Hemley and W. M. D'Angelo",1991,"Geochim. Cosmochim. Acta 55, 989-1004","annite: G and H revision for K-bearing silicates [after @SHD91]",https://doi.org/10.1016/0016-7037(89)90341-4
-JUN92,"C. de Capitani",1992,"JUN92.bs database supplied with Theriak/Domino software","data as listed in `JUN92.bs` data file",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html
-JOH92,"J. W. Johnson and E. H. Oelkers and H. C. Helgeson",1992,"Comp. Geosci. 18, 899-947",H<sub>2</sub>O,https://doi.org/10.1016/0098-3004(92)90029-Q
-Joh92,"J. W. Johnson",1992,"Personal calculation","steam: "Parameters given provide smooth metastable extrapolation of one-bar steam properties predicted by the @HGK84 equation of state to temperatures < the saturation temperature (99.632 C)."",
-SPRONS92.1,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","titanite: @BH83 + "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
-SPRONS92.2,"H. C. Helgeson et al.",1992,"sprons92.dat computer data file","Ca-bearing minerals; "Gibbs free energies and enthalpies were corrected to be consistent with updated values of Gibbs free energies of Ca<sup>2+</sup> and CO<sub>3</sub><sup>2-</sup> [@SH88] together with the solubilities of calcite and aragonite reported by @PB82 "",
-Sho92.1,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diketopiperazine GHS",https://doi.org/10.1016/0016-7037(92)90392-V
-VGT92,"O. Vidal, B. Goffé and T. Theye",1992,"J. Metamorphic Geol. 10, 603-614",sudoite,https://doi.org/10.1111/j.1525-1314.1992.tb00109.x
-ZS92,"C. Zhu and D. A. Sverjensky",1982,"Geochim. Cosmochim. Acta 56, 3435-3467","F,Cl,OH biotite and apatite endmembers. GHS and V were taken from Table 6 of @ZS92; heat capacity and volume parameters from `berman.dat`.",https://doi.org/10.1016/0016-7037(92)90390-5
-Sho93,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","ethylacetate and acetamide",https://doi.org/10.1016/0016-7037(93)90542-5
-Sho93.1,"E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3341-3349","carbon monoxide and ethylene",https://doi.org/10.1016/0016-7037(93)90542-5
-SK93,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","metal-acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J
-SK93.1,"E. L. Shock and C. M. Koretsky",1993,"Geochim. Cosmochim. Acta 57, 4899-4922","Ag-, Au-, Cu(I)- and Al-acetate complexes",https://doi.org/10.1016/0016-7037(93)90128-J
-SM93,"E. L. Shock and W. B. McKinnon",1993,"Icarus 106, 464-477","CO, HCN, urea",https://doi.org/10.1006/icar.1993.1185
-SS93,"M. D. Schulte and E. L. Shock",1993,"Geochim. Cosmochim. Acta 57, 3835-3846",aldehydes,https://doi.org/10.1016/0016-7037(93)90337-V
-HDM+94,"A. W. Hakin et al.",1994,"J. Chem. Soc., Faraday Trans. 90, 2027-2035","glutamic acid",https://doi.org/10.1039/FT9949002027
-HSS95,"J. R. Haas, E. L. Shock and D. C. Sassani",1995,"Geochim. Cosmochim. Acta 59, 4329-4350","complexes of rare earth elements",https://doi.org/10.1016/0016-7037(95)00314-P
-PH95,"V. A. Pokrovskii and H. C. Helgeson",1995,"Am. J. Sci. 295, 1255-1342","aluminum species",https://doi.org/10.2475/ajs.295.10.1255
-PK95,"V. B. Parker and I. L. Khodakovskii",1995,"J. Phys. Chem. Ref. Data 24, 1699-1745",melanterite,https://doi.org/10.1063/1.555964
-RH95,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bixbyite, cattierite, cerianite, chromite, cobalt, cobalt monoxide, guite, gypsum, hausmannite, huebnerite, linnaeite, manganese, manganosite, pyrolusite, willemite, wustite, zinc",https://doi.org/10.3133/b2131
-RH95.1,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","hydrogen fluoride and hydrogen chloride",https://doi.org/10.3133/b2131
-RH95.2,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","dawsonite: Cp coefficients corrected in @TKSS14; Cp value at 25 °C from @BPAH07, citing @FSR76",https://doi.org/10.3133/b2131
-RH95.3,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","almandine, dickite, glaucophane, grunerite, halloysite, pyrope: GHS and Cp at 25 °C",https://doi.org/10.3133/b2131
-RH95.4,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","fluorphlogopite (Al/Si disordered) (G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
-RH95.5,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","larnite (G and H not in SUPCRT92); Cp from @Kel60",https://doi.org/10.3133/b2131
-RH95.6,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","bromellite (melting temperature and G and H not in SUPCRT92)",https://doi.org/10.3133/b2131
-RH95.7,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","phase stability limit",https://doi.org/10.3133/b2131
-RH95.8,"R. A. Robie and B. S. Hemingway",1995,"U. S. Geological Survey Bull. 2131","brucite V",https://doi.org/10.3133/b2131
-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
-Sho95,"E. L. Shock",1995,"Am. J. Sci. 295, 496-580","carboxylic acids",https://doi.org/10.2475/ajs.295.5.496
-DPS+96,"I. Diakonov, G. Pokrovski et al.",1996,"Geochim. Cosmochim. Acta 60, 197-211",NaAl(OH)<sub>4</sub>,https://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
-DSM+97.1,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","phenol, and cresol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
-DSM+97.2,"J. D. Dale, E. L. Shock et al.",1997,"Geochim. Cosmochim. Acta 61, 4017-4024","dimethylphenol isomers",https://doi.org/10.1016/S0016-7037(97)00212-3
-HP97,"P. C. Ho and D. A. Palmer",1997,"Geochim. Cosmochim. Acta 61, 3027-3040",KOH,https://doi.org/10.1016/S0016-7037(97)00146-4
-MS97,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","MgSO<sub>4</sub>, NaSO<sub>4</sub><sup>-</sup>, and HCl",https://doi.org/10.1016/S0016-7037(97)00241-X
-MS97.1,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391",sulfur,https://doi.org/10.1016/S0016-7037(97)00241-X
-MS97.2,"T. M. McCollom and E. L. Shock",1997,"Geochim. Cosmochim. Acta 61, 4375-4391","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00241-X
-PH97,"V. A. Pokrovskii and H. C. Helgeson",1997,"Chem. Geol. 137, 221-242",KAl<sub>2</sub>O,https://doi.org/10.1016/S0009-2541(96)00167-2
-SSWS97,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","aqueous ions and hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0
-SSWS97.1,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","zincite and litharge",https://doi.org/10.1016/S0016-7037(96)00339-0
-SSWS97.2,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Au<sup>+</sup> and Cu<sup>+</sup>",https://doi.org/10.1016/S0016-7037(96)00339-0
-SSWS97.3,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","arsenate and arsenite species",https://doi.org/10.1016/S0016-7037(96)00339-0
-SSWS97.4,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Al<sup>+3</sup> and Al-hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0
-SSWS97.5,"E. L. Shock, D. C. Sassani et al.",1997,"Geochim. Cosmochim. Acta 61, 907-950","Zn<sup>+2</sup> and Zn-hydroxide complexes",https://doi.org/10.1016/S0016-7037(96)00339-0
-SSH97,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","metal complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
-SSH97.1,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au(HS)<sub>2</sub><sup>-</sup> and Ag(HS)<sub>2</sub><sup>-</sup>",https://doi.org/10.1016/S0016-7037(97)00009-4
-SSH97.2,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412",HSiO<sub>3</sub><sup>-</sup>,https://doi.org/10.1016/S0016-7037(97)00009-4
-SSH97.3,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Au-, Ag-, Cu- and Zn-chloride complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
-SSH97.4,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","Zn-acetate complexes",https://doi.org/10.1016/S0016-7037(97)00009-4
-SSH97.5,"D. A. Sverjensky, E. L. Shock and H. C. Helgeson",1997,"Geochim. Cosmochim. Acta 61, 1359-1412","NaHSiO<sub>3</sub>, CaHSiO<sub>3</sub><sup>+</sup>, and MgHSiO<sub>3</sub><sup>+</sup>",https://doi.org/10.1016/S0016-7037(97)00009-4
-SSB97,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266","uranium species",https://doi.org/10.1016/S0016-7037(97)00240-8
-SSB97.1,"E. L. Shock, D. C. Sassani and H. Betz",1997,"Geochim. Cosmochim. Acta 61, 4245-4266",uraninite,https://doi.org/10.1016/S0016-7037(97)00240-8
-TSD97,"Y. Tardy, R. Schaul, J. Duplay",1997,"C. R. Acad. Sci. Paris 324, 969-976","humic acid, microflora, and plants",https://doi.org/10.1016/S1251-8050(97)83981-X
-TZA97,"B. R. Tagirov, A. V. Zotov and N. N. Akinfiev",2007,"Geochim. Cosmochim. Acta 61, 4267-4280","aqueous HCl",https://doi.org/10.1016/S0016-7037(97)00274-3
-ST97,"D. Shvedov and P. R. Tremaine",1997,"J. Solution Chem. 26, 1113-1143","dimethylammonium chloride HKF parameters",https://doi.org/10.1023/A:1022977006327
-proton,OBIGT,1997,"Hydrogen-ion convention","""The conventional standard molal properties of the hydrogen ion are zero at any pressure and temperature"" [@JOH92]",https://chnosz.net
-HOKR98,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00219-6
-HOKR98.1,"H. C. Helgeson, C. E. Owens et al.",1998,"Geochim. Cosmochim. Acta 62, 985-1081","amino acids",https://doi.org/10.1016/S0016-7037(97)00219-6
-RH98,"L. Richard and H. C. Helgeson",1998,"Geochim. Cosmochim. Acta 62, 3591-3636","organic molecules and groups",https://doi.org/10.1016/S0016-7037(97)00345-1
-SLOP98.1,"E. L. Shock et al.",1998,"slop98.dat computer data file","zincite and litharge; "These data were used in @SSWS97, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools
-SLOP98.2,"E. L. Shock et al.",1998,"slop98.dat computer data file","daphnite; "G<sub>f</sub> and H<sub>f</sub> from @SS93a TMM"",http://geopig.asu.edu/?q=tools
-SLOP98.8,"E. L. Shock et al.",1998,"slop98.dat computer data file",""These data were used in @SK95, but were not tabulated in the paper."",http://geopig.asu.edu/?q=tools
-SLOP98.10,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Corrected values based on data from @HSS95 "",http://geopig.asu.edu/?q=tools
-SLOP98.11,"E. L. Shock et al.",1998,"slop98.dat computer data file",""Data and parameters as used by @MS97. "",http://geopig.asu.edu/?q=tools
-SS98a,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group ions and complexes",https://doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.1,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","platinum-group solids",https://doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.2,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671",Rh<sup>+3</sup>,https://doi.org/10.1016/S0016-7037(98)00049-0
-SS98a.3,"D. C. Sassani and E. L. Shock",1998,"Geochim. Cosmochim. Acta 62, 2643-2671","Pd<sup>+2</sup> and Pt<sup>+2</sup> and their complexes",https://doi.org/10.1016/S0016-7037(98)00049-0
-SUF+98,"H. Senoh et al.",1998,"J. Alloys Compd. 280, 114-124","Mn(OH)<sub>2</sub>: Cp coefficients from linear fit to values estimated by @SUF+98",https://doi.org/10.1016/S0925-8388(98)00739-7
-HS99,"J. R. Haas and E. L. Shock",1998,"Geochim. Cosmochim. Acta 63, 3429-3441","chloroethylene species",https://doi.org/10.1016/S0016-7037(99)00276-8
-MS99,"W. M. Murphy and E. L. Shock",1999,"Rev. Mineral. Geochem. 38, 221-253","americium species",http://rimg.geoscienceworld.org/content/38/1/221
-PSK99,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","metal-dicarboxylate complexes",https://doi.org/10.1016/S0016-7037(99)00146-5
-PSK99.1,"P. Prapaipong, E. L. Shock and C. M. Koretsky",1999,"Geochim. Cosmochim. Acta 63, 2547-2577","Al(Mal)<sup>+</sup> and Al(Oxal)<sup>+</sup>",https://doi.org/10.1016/S0016-7037(99)00146-5
-SAJ00,"R. E. Stoffregen, C. N. Alpers and J. L. Jambor",2000,"Rev. Mineral. Geochem. 40, 453-479","jarosite, natroalunite, and natrojarosite",https://doi.org/10.2138/rmg.2000.40.9
-TDDZ00,"B. R. Tagirov et al.",2000,"Chem. Geol. 162, 193-219",FeCl<sup>+2</sup>,https://doi.org/10.2138/rmg.2000.40.9
-WS00,"S. A. Wood and I. M. Samson",2000,"Econ. Geol. 95, 143-182","scheelite and ferberite; GHS and V of scheelite and V of ferberite are from @RHF78.",https://doi.org/10.2113/gsecongeo.95.1.143
-AP01,"J. P. Amend and A. V. Plyasunov",2001,"Geochim. Cosmochim. Acta 65, 3901-3917",carbohydrates,https://doi.org/10.1016/S0016-7037(01)00707-4
-AS01,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","NO and N<sub>2</sub>O",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x
-AS01.1,"J. P. Amend and E. L. Shock",2001,"FEMS Microbiol. Rev. 25, 175-243","selenium and molybdenite",https://doi.org/10.1111/j.1574-6976.2001.tb00576.x
-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
[TRUNCATED]
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svnlook diff /svnroot/chnosz -r 858
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