[CHNOSZ-commits] r247 - in pkg/CHNOSZ: . R data demo inst/extdata/Berman inst/extdata/OBIGT tests/testthat vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 9 01:36:33 CEST 2017
Author: jedick
Date: 2017-10-09 01:36:32 +0200 (Mon, 09 Oct 2017)
New Revision: 247
Added:
pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/berman.R
pkg/CHNOSZ/data/refs.csv
pkg/CHNOSZ/demo/DEW.R
pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv
pkg/CHNOSZ/tests/testthat/test-berman.R
pkg/CHNOSZ/vignettes/obigt.Rmd
pkg/CHNOSZ/vignettes/obigt.bib
Log:
update some thermodynamic data and references
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/DESCRIPTION 2017-10-08 23:36:32 UTC (rev 247)
@@ -1,6 +1,6 @@
-Date: 2017-10-08
+Date: 2017-10-09
Package: CHNOSZ
-Version: 1.1.0-45
+Version: 1.1.0-46
Title: Thermodynamic Calculations for Geobiochemistry
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/R/berman.R
===================================================================
--- pkg/CHNOSZ/R/berman.R 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/R/berman.R 2017-10-08 23:36:32 UTC (rev 247)
@@ -19,8 +19,10 @@
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)
+ 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(JUN92, ZS92, SHD91, Ber90, Ber88)
+ dat <- rbind(BDat17, FDM14, JUN92, ZS92, SHD91, Ber90, Ber88)
# remove duplicates (only the first, i.e. latest entry is kept)
dat <- dat[!duplicated(dat$name), ]
# remove the multipliers
Modified: pkg/CHNOSZ/data/refs.csv
===================================================================
--- pkg/CHNOSZ/data/refs.csv 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/data/refs.csv 2017-10-08 23:36:32 UTC (rev 247)
@@ -24,14 +24,15 @@
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
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
+SH90.1,"E. L. Shock and H. C. Helgeson",1990,"Geochim. Cosmochim. Acta 54, 915-945","formic acid, formate, and propanoate",https://doi.org/10.1016/0016-7037(90)90429-O
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 database",http://titan.minpet.unibas.ch/minpet/theriak/theruser.html
+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
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,"E. L. Shock",1992,"Geochim. Cosmochim. Acta 56, 3481-3491","diglycine, alanylglycine, leucylglycine, and diketopiperazine",https://doi.org/10.1016/0016-7037(92)90392-V
-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` in SUPCRT92b.zip file on the [DEW website](http://www.dewcommunity.org/resources.html).",https://doi.org/10.1016/0016-7037(92)90390-5
+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
@@ -77,7 +78,7 @@
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
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",https://doi.org/10.1016/S0016-7037(01)00678-0
-PS01.1,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","acetic acid and methane",https://doi.org/10.1016/S0016-7037(01)00678-0
+PS01.1,"A. V. Plyasunov and E. L. Shock",2001,"Geochim. Cosmochim. Acta 65, 3879-3900","acetic acid, propanoic acid, and methane",https://doi.org/10.1016/S0016-7037(01)00678-0
Ric01,"L. Richard",2001,"Geochim. Cosmochim. Acta 65, 3827-3877","organic sulfur compounds",https://doi.org/10.1016/S0016-7037(01)00761-X
SSW01,"M. D. Schulte, E. L. Shock and R. H. Wood",2001,"Geochim. Cosmochim. Acta 65, 3919-3930","AsH<sub>3</sub>, CF<sub>4</sub>, CH<sub>3</sub>F, Cl<sub>2</sub>, ClO<sub>2</sub>, N<sub>2</sub>O, NF<sub>3</sub>, NO, PH<sub>3</sub>, and SF<sub>6</sub>",https://doi.org/10.1016/S0016-7037(01)00717-7
MGN03,"J. Majzlan, K.-D. Grevel and A. Navrotsky",2003,"Am. Mineral. 88, 855-859","goethite, lepidocrocite, and maghemite GHS",https://doi.org/10.2138/am-2003-5-614
@@ -111,6 +112,7 @@
LD12.3,"D. E. LaRowe and J. M. Dick",2012,"Geochim. Cosmochim. Acta 80, 70-91","methionine sidechain GHS",https://doi.org/10.1016/j.gca.2011.11.041
DEH+13,"J. M. Dick, K. A. Evans et al.",2013,"Geochim. Cosmochim. Acta 122, 247-266","phenanthrene and methylphenanthrene isomers",https://doi.org/10.1016/j.gca.2013.08.020
FDM+14,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","CO<sub>2</sub>, CO<sub>3</sub><sup>-2</sup>, and HCO<sub>3</sub><sup>-</sup>",https://doi.org/10.1016/j.gca.2014.01.030
+FDM+14.1,"S. Facq et al.",2014,"Geochim. Cosmochim. Acta 132, 375-390","aragonite; source of data: `berman.dat`",https://doi.org/10.1016/j.gca.2014.01.030
SHA14,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","SiO<sub>2</sub> and Si<sub>2</sub>O<sub>4</sub>",https://doi.org/10.1016/j.gca.2013.12.019
SHA14.1,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","revisions for AlO<sub>2</sub><sup>-</sup> and HAlO<sub>2</sub>",https://doi.org/10.1016/j.gca.2013.12.019
SHA14.2,"D. A. Sverjensky et al.",2014,"Geochim. Cosmochim. Acta 129, 125-145","revisions for BO(OH) and BO<sub>2</sub><sup>-</sup>",https://doi.org/10.1016/j.gca.2013.12.019
@@ -133,7 +135,7 @@
CHNOSZ.7,"J. M. Dick",2017,"CHNOSZ package documentation","charge of NpO2(Oxal), La(Succ)+, NH4(Succ)-, and NpO2(Succ) as listed by @PSK99",http://chnosz.net
CHNOSZ.8,"J. M. Dick",2017,"CHNOSZ package documentation","Incorrect values of HKF a<sub>1</sub>--a<sub>4</sub> parameters for [-CH2NH2] were printed in Table 6 of @DLH06; corrected values are used here.",http://chnosz.net
LCT17,"A. R. Lowe, J. S. Cox and P. R. Tremaine",2017,"J. Chem. Thermodynamics 112, 129-145","adenine Cp and V",https://doi.org/10.1016/j.jct.2017.04.005
-DEW17,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","data from Aqueous Species Table in spreadsheet (see detailed references there)",http://www.dewcommunity.org
+DEW17,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","other data from Aqueous Species Table in spreadsheet (see detailed references there)",http://www.dewcommunity.org
DEW17.1,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for ions",http://www.dewcommunity.org
DEW17.2,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for cations",http://www.dewcommunity.org
DEW17.3,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","revised with new predicted a1 for complex species",http://www.dewcommunity.org
@@ -165,7 +167,6 @@
DEW17.32,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaOH: Fitted to Ho & Palmer (1997) data with a1 pred. from the sum of the ions and used to predict the volume",http://www.dewcommunity.org
DEW17.33,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","OH-: August 16th, 2013 fit to Bandura & Lvov (2005)",http://www.dewcommunity.org
DEW17.34,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","propane: Shock & Helgeson (1990) with new a1-a4 based on revised correlation to predict a1 in Sverjensky et al. (2013)",http://www.dewcommunity.org
-DEW17.35,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","propanoate: Revised a1 from new delVn correlation for -1 ions; kept original regression c1 and c2 plus omega from Shock & Helgeson (1990)",http://www.dewcommunity.org
DEW17.36,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","S3-: Regression of data from Pokrovski & Dubessy (2015), Guggenheim (1971); Feb. 2015",http://www.dewcommunity.org
DEW17.38,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","SO2: Shock et al. (1989) with revised a1 predicted as a complex from delVn",http://www.dewcommunity.org
DEW17.39,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","toluene: Plyasunov & Shock (2001) with new a1 to a4 predicted with revised a1 consistent with Sverjensky et al. (2013)",http://www.dewcommunity.org
@@ -173,3 +174,5 @@
DEW17.101,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","methane: revised with new predicted a1 for complex species",http://www.dewcommunity.org
DEW17.102,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","MgCl<sup>+</sup>: revised volume increased in order that a1 of the complex is the sum of the a1 values of the ions",http://www.dewcommunity.org
DEW17.103,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","NaCl: revised with new predicted a1 for complex species",http://www.dewcommunity.org
+DEW17.104,"D. A. Sverjensky et al.",2017,"Deep Earth Water (DEW) spreadsheet","propanoate: Revised a1 from new delVn correlation for -1 ions",http://www.dewcommunity.org
+BDat17.1,"D. A. Sverjensky et al.",2017,"berman.dat file in SUPCRT92b.zip on the DEW website","antigorite: "Oct. 21, 2016: Revised volume coefficients consistent with @HDR06 and @YIY+14 "",http://www.dewcommunity.org/resources.html
Modified: pkg/CHNOSZ/demo/DEW.R
===================================================================
--- pkg/CHNOSZ/demo/DEW.R 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/demo/DEW.R 2017-10-08 23:36:32 UTC (rev 247)
@@ -6,9 +6,11 @@
# activate DEW model
oldwat <- water("DEW")
+###########
#### plot 1: quartz solubility at high pressure
## after Figure 7D of Sverjensky et al., 2014a [SHA14]
## (Geochim. Cosmochim. Acta, https://doi.org/10.1016/j.gca.2013.12.019)
+###########
# load SiO2 and Si2O4 data taken from DEW spreadsheet
iSi <- add.obigt("DEW_aq", c("SiO2", "Si2O4"))
@@ -46,8 +48,11 @@
# TODO: lines are a little low at highest P and P ...
# does the Berman, 1988 quartz data increase high-PT solubilities?
+###########
#### plot 2: correlations between non-solvation volume and HKF a1 parameter
## after Figures 12B and 12C of Sverjensky et al., 2014a [SHA14]
+###########
+
# load the fitted parameters for species as used by SHA14
# TODO: also use their Ca+2??
# NOTE: don't load NaCl, NH4+, or HS- here because the DEW spreadsheet lists a1 from the correlation
@@ -85,9 +90,11 @@
t2 <- quote("volume and HKF "*italic(a)[1]*" parameter")
mtitle(as.expression(c(t1, t2)))
-#### plot 3: aqueous inorganic and organic carbon species at high pressure
+###########
+#### plot 3: logfO2-pH diagram for aqueous inorganic and organic carbon species at high pressure
## after Figure 1b of Sverjensky et al., 2014b [SSH14]
## (Nature Geoscience, https://doi.org/10.1038/NGEO2291)
+###########
# define system with loga.species = 0
basis("CHNOS+")
@@ -115,12 +122,16 @@
DEWexpr <- substitute("DEW data for"~x, list(x=CO2quote))
mtitle(as.expression(c(DEWexpr, "and methane")))
-#### plot 4: after SSH14 Fig. 3 (added 20171008)
+###########
+#### plot 4: speciation of carbon as a function T, logfO2 and pH (added 20171008)
+## after SSH14 Fig. 3
+###########
+
# conditions:
# T = 600, 700, 800, 900, 1000 degC
# P = 5.0GPa (50000 bar)
# fO2 = QFM - 2
-# pH set by jadeite + kyanite + coesite
+# pH set by jadeite + kyanite + coesite (approximated here as constant)
# dissolved carbon 0.03, 0.2, 1, 4, 20 molal
T <- seq(600, 1000, 5)
@@ -135,16 +146,14 @@
# skip updating acetate because the new data from the DEW spreadsheet give different logK
add.obigt("DEW", c(inorganics, organics[-4]))
## set basis species
-b.species <- c("Fe", "CO3-2", "H2O", "O2", "SiO2", "H+")
-b.state <- c("cr", "aq", "liq", "gas", "aq", "aq")
-basis(b.species, b.state)
+basis(c("Fe", "SiO2", "CO3-2", "H2O", "oxygen", "H+"))
# for the time being we use a constant pH
basis("H+", -4)
-## define a QFM buffer using Berman minerals
+## define a QFM buffer using Berman's equations for minerals
mod.buffer("QFM_Berman", c("quartz", "fayalite", "magnetite"), "cr_Berman", 0)
-## calculate fO2 in QFM buffer minus 2
+## calculate logfO2 as QFM minus 2
basis("O2", "QFM_Berman")
a <- affinity(T=T, P=50000, return.buffer=TRUE)
QFM_2 <- a$O2 - 2
@@ -181,7 +190,7 @@
t2 <- "after Sverjensky et al., 2014b"
mtitle(c(t1, t2))
-### additional checks
+## additional checks
# check that we're within 0.1 of the QFM-2 values used by SSH14
stopifnot(maxdiff(QFM_2[T %% 100 == 0], c(-17.0, -14.5, -12.5, -10.8, -9.4)) < 0.1)
# Here are the logKs of aqueous species dissociation reactions at 600 degC and 50000 bar,
@@ -194,8 +203,9 @@
# check that we're within 0.021 of the logK values used by SSH14
stopifnot(maxdiff(logK.calc, c(inorganic.logK, organic.logK)) < 0.021)
-#############
+###########
### all done!
# reset the database and previous water computational option
data(OBIGT)
water(oldwat)
+###########
Added: pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/BDat17.csv 2017-10-08 23:36:32 UTC (rev 247)
@@ -0,0 +1,2 @@
+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
+antigorite,-66076529,-71364156,3602.996,174.246,7394.51,0,-5483.63,8728.412,-1.485,4,27.2,80,,,,,,,,,,,,,,
Added: pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv (rev 0)
+++ pkg/CHNOSZ/inst/extdata/Berman/FDM+14.csv 2017-10-08 23:36:32 UTC (rev 247)
@@ -0,0 +1,2 @@
+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
+aragonite,-1128353.67,-1207213.7,88.7,3.42,195,-21,-0.1,22,-1.345,1.7,41.8,0,,,,,,,,,,,,,,
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv.xz
===================================================================
(Binary files differ)
Modified: pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/DEW_aq.csv 2017-10-08 23:36:32 UTC (rev 247)
@@ -57,8 +57,8 @@
FeCl3,FeCl3(0),FeCl3,aq,DEW17,NA,26.Sep.17,-99307,-134400,18,-28,37.4,8.927750435512179,4.2169678004086695,1.3022132117708338,-2.9533294488688946,-7.4792707212502485,-8.738199999999999,0.3,0
FeCl4-,FeCl4(-),FeCl4-,aq,DEW17,NA,26.Sep.17,-127917,-180057,26,-95.9,55.8,12.950315210745682,8.046848504824029,-1.9091054640732654,-3.1116567171894256,-38.64687843457357,-22.56943,1.2363,-1
FeO,FeO(0),FeO,aq,DEW17,NA,26.Sep.17,-50720,,-10,0,3,2.246926435512177,-2.1438393852779156,6.635689757212449,-2.6903736798126108,8.930455103006798,-3.0346,0.3,0
-formate,FORMATE,HCOO-,aq,DEW17,NA,26.Sep.17,-83862,-101680,21.7,-20.177464600379487,26.159971565219035,5.268366909492395,7.6836443146635105,3.4705805840890083,-3.0966418559681896,17,-12.4,1.3003,-1
-"formic acid",FORMIC-ACID,HCOOH,aq,DEW17,NA,26.Sep.17,-88982,-101680,38.9,19.024124873651285,34.69001430971288,8.092450502078368,3.4216794020330656,1.9690549970623223,-2.920452226480047,22.1924,-3.1196,-0.3442,0
+formate,FORMATE,HCOO-,aq,SH90.1,DEW17.1,26.Sep.17,-83862,-101680,21.7,-20.177464600379487,26.159971565219035,5.268366909492395,7.6836443146635105,3.4705805840890083,-3.0966418559681896,17,-12.4,1.3003,-1
+"formic acid",FORMIC-ACID,HCOOH,aq,SH90.1,DEW17.3,26.Sep.17,-88982,-101680,38.9,19.024124873651285,34.69001430971288,8.092450502078368,3.4216794020330656,1.9690549970623223,-2.920452226480047,22.1924,-3.1196,-0.3442,0
Ga+3,Ga(+3),Ga+3,aq,DEW17,NA,26.Sep.17,-38000,-50600,-79,-30.799816226244204,-44.900021278327145,-9.112600703984713,-1.513730145487252,14.464344791566415,-2.7164223957855573,13.244942645072129,-9.308522565285944,2.7276,3
Gd+3,Gd(+3),Gd+3,aq,DEW17,NA,26.Sep.17,-158600,-164200,-49.2,-35.899991514322814,-40.400091694714845,-7.815913141749289,-2.4648289055059194,13.665950891634948,-2.6771039730463855,6.560657450392803,-10.347428271467557,2.3265,3
glutamate,GLUTAMATE,C5H8NO4-,aq,DEW17,NA,26.Sep.17,-167258,0,44.4,11.10918772896642,79.70753937846106,17.46,12.34,-5.51,-3.29,50,-14.8,0.9569,-1
@@ -148,7 +148,7 @@
PO4-3,PO4(-3),PO4-3,aq,DEW17,NA,26.Sep.17,-243500,-305300,-53,-114.89996391595473,-30.600095804682038,-1.1970758608927012,-7.319635964606203,9.590613498435385,-2.4764062492231798,-9.47495397363052,-26.43972264967998,5.6114,-3
Pr+3,Pr(+3),Pr+3,aq,DEW17,NA,26.Sep.17,-162600,-168800,-50,-47.69967108409179,-42.09999378698761,-8.527528167362654,-1.9428711200045896,14.104105087060267,-2.69868170789901,-1.197656471892774,-12.751022999829498,2.235,3
propane,PROPANE,C3H8,aq,DEW17,NA,26.Sep.17,-1963,-30490,33.37,110.59958327471779,66.99993622090898,14.290088050581724,9.322445153802782,-2.9786811657360044,-3.1643898826582073,66.32953185662123,19.49453511306001,-0.5053,0
-propanoate,PROPANOATE,C2H5COO-,aq,DEW17,NA,26.Sep.17,-86770,-122630,26.5,32.45551213710533,54.950066467724966,8.378618967437145,19.33650894227708,0.04597812207649099,-3.5783712796737346,52.3,-4.2,1.2276,-1
+propanoate,PROPANOATE,C2H5COO-,aq,SH90.1,DEW17.104,26.Sep.17,-86770,-122630,26.5,32.45551213710533,54.950066467724966,8.378618967437145,19.33650894227708,0.04597812207649099,-3.5783712796737346,52.3,-4.2,1.2276,-1
"propanoic acid",PROPANOIC-ACID,C3H6O2,aq,DEW17,NA,26.Sep.17,-93450,-122470,49.4,61.28421794436844,68.27064151281941,14.6,7.9,6.9,-4.3,63.3,-1.4,-0.09,0
propanol,PROPANOL,C3H7OH,aq,DEW17,NA,26.Sep.17,-41910,-75320,40.6,82.84849041327438,70.88199974121683,14.6,9.1,12.2,-5.5,74.3,3.3,-0.2,0
Ra+2,Ra(+2),Ra+2,aq,DEW17,NA,26.Sep.17,-134200,-126100,13,-14.40028139320611,-10.59999289581294,1.5462375047327335,-8.634006964911572,7.8259092280446785,-2.422070152070556,6.285875837483136,-5.967937319796084,0.929,2
Modified: pkg/CHNOSZ/tests/testthat/test-berman.R
===================================================================
--- pkg/CHNOSZ/tests/testthat/test-berman.R 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/tests/testthat/test-berman.R 2017-10-08 23:36:32 UTC (rev 247)
@@ -7,8 +7,11 @@
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)
+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(ZS92, SHD91, Ber90, Ber88)
+dat <- rbind(BDat17, FDM14, JUN92, ZS92, SHD91, Ber90, Ber88)
dat <- dat[!duplicated(dat$name), ]
mineral <- unique(dat$name)
prop_Berman <- NULL
@@ -16,9 +19,7 @@
test_that("properties of all minerals are computed without warnings", {
# running this without error means that:
# - formulas for the minerals are found in thermo$obigt
- # - there are no warnings for minerals with GfPrTr(calc) >= 1000 J/cal different from GfPrTr(table)
- #expect_silent(properties <- lapply(mineral, berman, check.G=TRUE))
- # - warnings are produced for 3 minerals with GfPrTr(calc) >= 1000 J/cal different from GfPrTr(table)
+ # - warnings are produced for mineral(s) with GfPrTr(calc) >= 1000 J/cal different from GfPrTr(table)
expect_warning(properties <- lapply(mineral, berman, check.G=TRUE),
"fluortremolite", all=TRUE)
# save the results so we can use them in the next tests
@@ -55,11 +56,11 @@
# which minerals differ in Cp by more than 4 cal/K/mol?
idiffCp <- which(abs(prop_Berman$Cp - prop_Helgeson$Cp) > 4)
- expect_match(mineral[idiffCp], "antigorite|cristobalite,beta|K-feldspar|fluortremolite")
+ expect_match(mineral[idiffCp], "glaucophane|antigorite|cristobalite,beta|K-feldspar|fluortremolite")
# which minerals differ in V by more than 1 cm^3/mol?
idiffV <- which(abs(prop_Berman$V - prop_Helgeson$V) > 1)
- expect_match(mineral[idiffV], "anthophyllite|antigorite|chrysotile|merwinite")
+ expect_match(mineral[idiffV], "glaucophane|anthophyllite|antigorite|chrysotile|merwinite")
})
test_that("high-T,P calculated properties are similar to precalculated ones", {
Modified: pkg/CHNOSZ/vignettes/obigt.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.Rmd 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/vignettes/obigt.Rmd 2017-10-08 23:36:32 UTC (rev 247)
@@ -117,10 +117,12 @@
Any secondary references (`ref2`) are listed with bullet points.
Each reference is followed by the number of species, and a note (from `thermo$refs`).
Symbols show whether the data were present in the earliest of the sprons92.dat (ø), slop98.dat (\*), slop07.dat (†), or slop15.dat (‡) datafiles for the SUPCRT92 package.
+NOTE: URLs for the slop files and other data files cited below (`JUN92.bs`, `berman.dat`, and the DEW model spreadsheet) are given in the References.
Any additional comments are placed at the beginning of the sections.
-Abbreviations used below are: Cp (heat capacity), GHS (standard Gibbs energy, enthalpy, entropy), HKF (Helgeson-Kirkham-Flowers equations), *V* (volume), *T* (temperature), *P* (pressure).
+Abbreviations used below are: Cp (heat capacity), GHS (standard Gibbs energy, enthalpy, entropy), HKF (Helgeson-Kirkham-Flowers equations), V (volume), T (temperature), P (pressure).
+
# Recent additions (late 2017)
* Mineral data using the [Berman (1988)]() equations are listed under **Solids** / **Berman**.
Modified: pkg/CHNOSZ/vignettes/obigt.bib
===================================================================
--- pkg/CHNOSZ/vignettes/obigt.bib 2017-10-08 14:27:06 UTC (rev 246)
+++ pkg/CHNOSZ/vignettes/obigt.bib 2017-10-08 23:36:32 UTC (rev 247)
@@ -1014,15 +1014,48 @@
}
@Article{Kul06,
- author = {Kulik, D. A.},
- journal = {Chemical Geology},
- title = {{D}ual-thermodynamic estimation of stoichiometry and stability of solid solution end members in aqueous–solid solution systems},
+ author = {Kulik, D. A.},
+ journal = {Chemical Geology},
+ title = {{D}ual-thermodynamic estimation of stoichiometry and stability of solid solution end members in aqueous–solid solution systems},
+ year = {2006},
+ volume = {225},
+ number = {3},
+ pages = {189--212},
+ note = {Solid solutions: from theory to experiment},
+ doi = {10.1016/j.chemgeo.2005.08.014},
+ issn = {0009-2541},
+}
+
+ at Misc{BDat17,
+ author = {berman.dat},
+ title = {{D}ata file in {SUPCRT}92b.zip on the {DEW} website},
+ howpublished = {Last updated on 2017-02-03. Accessed on 2017-05-04.},
+ year = {2017},
+ url = {http://www.dewcommunity.org/resources.html},
+}
+
+ at Article{HDR06,
+ author = {Hilairet, Nadège and Daniel, Isabelle and Reynard, Bruno},
+ journal = {Geophysical Research Letters},
+ title = {{E}quation of state of antigorite, stability field of serpentines, and seismicity in subduction zones},
year = {2006},
- volume = {225},
- number = {3},
- pages = {189--212},
- note = {Solid solutions: from theory to experiment},
- doi = {10.1016/j.chemgeo.2005.08.014},
- issn = {0009-2541},
+ volume = {33},
+ number = {2},
+ pages = {L02302},
+ doi = {10.1029/2005GL024728},
+ issn = {1944-8007},
}
+ at Article{YIY+14,
+ author = {Yang, Cuiping and Inoue, Toru and Yamada, Akihiro and Kikegawa, Takumi and Ando, Jun-ichi},
+ journal = {Physics of the Earth and Planetary Interiors},
+ title = {{E}quation of state and phase transition of antigorite under high pressure and high temperature},
+ year = {2014},
+ volume = {228},
+ number = {Supplement C},
+ pages = {56--62},
+ note = {High-Pressure Research in Earth Science: Crust, Mantle, and Core},
+ doi = {10.1016/j.pepi.2013.07.008},
+ issn = {0031-9201},
+}
+
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