[CHNOSZ-commits] r743 - in pkg/CHNOSZ: . R inst inst/extdata/Berman/testing inst/extdata/adds inst/tinytest man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Sep 19 11:32:39 CEST 2022
Author: jedick
Date: 2022-09-19 11:32:39 +0200 (Mon, 19 Sep 2022)
New Revision: 743
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/R/add.OBIGT.R
pkg/CHNOSZ/inst/NEWS.Rd
pkg/CHNOSZ/inst/extdata/Berman/testing/BA96_OBIGT.csv
pkg/CHNOSZ/inst/extdata/adds/BZA10.csv
pkg/CHNOSZ/inst/extdata/adds/SK95.csv
pkg/CHNOSZ/inst/tinytest/test-util.data.R
pkg/CHNOSZ/man/add.OBIGT.Rd
Log:
Remove back-compatibility for OBIGT data files without an 'E_units' column
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/DESCRIPTION 2022-09-19 09:32:39 UTC (rev 743)
@@ -1,6 +1,6 @@
Date: 2022-09-19
Package: CHNOSZ
-Version: 1.9.9-34
+Version: 1.9.9-35
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 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/R/add.OBIGT.R 2022-09-19 09:32:39 UTC (rev 743)
@@ -117,10 +117,8 @@
# isys <- which(file==sysnostate)
# if(length(isys)==1) file <- system.file(paste0("extdata/OBIGT/", sysfiles[isys]), package="CHNOSZ")
# }
- # Tead data from the file
+ # Read data from the file
to2 <- read.csv(file, as.is=TRUE)
- # Add E_units column if it's missing 20190529
- if(!"E_units" %in% colnames(to2)) to2 <- data.frame(to2[, 1:8], E_units = "cal", to2[, 9:21], stringsAsFactors = FALSE)
Etxt <- paste(unique(to2$E_units), collapse = " and ")
# Load only selected species if requested
if(!is.null(species)) {
@@ -132,7 +130,7 @@
id2 <- paste(to2$name,to2$state)
# Check if the data is compatible with thermo$OBIGT
tr <- tryCatch(rbind(to1, to2), error = identity)
- if(inherits(tr, "error")) stop(paste(file, "is not compatible with thermo$OBIGT data table."))
+ if(inherits(tr, "error")) stop(paste(file, "is not compatible with thermo$OBIGT data frame."))
# Match the new species to existing ones
does.exist <- id2 %in% id1
ispecies.exist <- na.omit(match(id2, id1))
Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/inst/NEWS.Rd 2022-09-19 09:32:39 UTC (rev 743)
@@ -12,7 +12,7 @@
% links to vignettes 20220723
\newcommand{\viglink}{\ifelse{html}{\out{<a href="../CHNOSZ/doc/#1.html"><strong>#1.Rmd</strong></a>}}{\bold{#1.Rmd}}}
-\section{Changes in CHNOSZ version 1.9.9-34 (2022-09-19)}{
+\section{Changes in CHNOSZ version 1.9.9-35 (2022-09-19)}{
\subsection{MAJOR USER-VISIBLE CHANGES}{
\itemize{
@@ -28,9 +28,12 @@
read using \code{add.OBIGT()} must have this column; there is no
back-compatibility support for data files in the older format.
+ \item Backward compatibility for OBIGT data files without an
+ \code{E_units} column has been removed.
+
\item Units of Joules instead of calories are now used by default for the
thermodynamic properties output by \code{subcrt()}. That is,
- \code{E.units("J")} is the default setting. User scripts that implicitly
+ \code{E.units("J")} is the default setting. Scripts that implicitly
depend on the previous default setting of \code{E.units("cal")} may need
to be modified to produce expected output.
Modified: pkg/CHNOSZ/inst/extdata/Berman/testing/BA96_OBIGT.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/Berman/testing/BA96_OBIGT.csv 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/inst/extdata/Berman/testing/BA96_OBIGT.csv 2022-09-19 09:32:39 UTC (rev 743)
@@ -1,21 +1,21 @@
-name,abbrv,formula,state,ref1,ref2,date,model,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-almandine,Alm,Si3Fe3Al2O12,cr,BA96.1,NA,03.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-anthophyllite,Ath,Mg7Si8O24H2,cr,BA96.1,NA,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-cordierite,Cd,Mg2Al4Si5O18,cr,Ber88,BA96.2,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-enstatite,En,MgSiO3,cr,Ber88,BA96.2,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-fayalite,Fa,Fe2SiO4,cr,BA96.1,NA,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ferrosilite,Fsl,SiFeO3,cr,BA96.1,NA,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-forsterite,Fo,Mg2SiO4,cr,Ber88,BA96.3,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hematite,Hm,Fe2O3,cr,Ber88,BA96.2,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-ilmenite,Ilm,FeTiO3,cr,Ber88,BA96.4,03.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-magnetite,Mt,Fe3O4,cr,Ber88,BA96.2,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-pyrope,Py,Mg3Al2Si3O12,cr,Ber88,BA96.3,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-rutile,Rt,TiO2,cr,Ber88,BA96.2,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-spinel,Sp,MgAl2O4,cr,Ber88,BA96.3,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-talc,Tc,Mg3Si4O12H2,cr,Ber88,BA96.4,01.Oct.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-Fe-cordierite,fCd,Fe2Al4Si5O18,cr,BA96,NA,12.Dec.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-geikelite,Gk,MgTiO3,cr,BA96,NA,12.Dec.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-hercynite,Hc,FeAl2O4,cr,BA96,NA,12.Dec.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-iron-a,aFe,Fe,cr,BA96,NA,12.Dec.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-iron-g,gFe,Fe,cr,BA96,NA,12.Dec.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-orthocorundum,Ok,Al2O3,cr,BA96,NA,12.Dec.17,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+name,abbrv,formula,state,ref1,ref2,date,E_units,model,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+almandine,Alm,Si3Fe3Al2O12,cr,BA96.1,NA,03.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+anthophyllite,Ath,Mg7Si8O24H2,cr,BA96.1,NA,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+cordierite,Cd,Mg2Al4Si5O18,cr,Ber88,BA96.2,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+enstatite,En,MgSiO3,cr,Ber88,BA96.2,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+fayalite,Fa,Fe2SiO4,cr,BA96.1,NA,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ferrosilite,Fsl,SiFeO3,cr,BA96.1,NA,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+forsterite,Fo,Mg2SiO4,cr,Ber88,BA96.3,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hematite,Hm,Fe2O3,cr,Ber88,BA96.2,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+ilmenite,Ilm,FeTiO3,cr,Ber88,BA96.4,03.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+magnetite,Mt,Fe3O4,cr,Ber88,BA96.2,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+pyrope,Py,Mg3Al2Si3O12,cr,Ber88,BA96.3,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+rutile,Rt,TiO2,cr,Ber88,BA96.2,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+spinel,Sp,MgAl2O4,cr,Ber88,BA96.3,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+talc,Tc,Mg3Si4O12H2,cr,Ber88,BA96.4,01.Oct.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+Fe-cordierite,fCd,Fe2Al4Si5O18,cr,BA96,NA,12.Dec.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+geikelite,Gk,MgTiO3,cr,BA96,NA,12.Dec.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+hercynite,Hc,FeAl2O4,cr,BA96,NA,12.Dec.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-a,aFe,Fe,cr,BA96,NA,12.Dec.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+iron-g,gFe,Fe,cr,BA96,NA,12.Dec.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+orthocorundum,Ok,Al2O3,cr,BA96,NA,12.Dec.17,J,Berman,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
Modified: pkg/CHNOSZ/inst/extdata/adds/BZA10.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/BZA10.csv 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/inst/extdata/adds/BZA10.csv 2022-09-19 09:32:39 UTC (rev 743)
@@ -1,5 +1,5 @@
-name,abbrv,formula,state,ref1,ref2,date,model,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-CdCl+,NA,CdCl+,aq,BZA10,NA,2010-07-03,HKF,-52629,NA,7.06,11.12,2.2,2.2303,-2.3357,6.6681,-2.6824,16.6723,-0.7693,0.4372,1
-CdCl2,NA,CdCl2,aq,BZA10,NA,2010-07-03,HKF,-84883,NA,25.72,116.01,42.21,7.5221,10.5852,1.5895,-3.2166,73.7023,20.5956,-0.0495,0
-CdCl3-,NA,CdCl3-,aq,BZA10,NA,2010-07-03,HKF,-115399,NA,45.15,97.78,63.47,10.8045,18.5994,-1.5605,-3.5479,72.0244,16.8832,0.9378,-1
-CdCl4-2,NA,CdCl4-2,aq,BZA10,NA,2010-07-03,HKF,-145583,NA,50.61,42.52,81.35,13.8329,25.9938,-4.4669,-3.8536,53.6766,5.6267,2.4766,-2
+name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+CdCl+,NA,CdCl+,aq,BZA10,NA,2010-07-03,HKF,cal,-52629,NA,7.06,11.12,2.2,2.2303,-2.3357,6.6681,-2.6824,16.6723,-0.7693,0.4372,1
+CdCl2,NA,CdCl2,aq,BZA10,NA,2010-07-03,HKF,cal,-84883,NA,25.72,116.01,42.21,7.5221,10.5852,1.5895,-3.2166,73.7023,20.5956,-0.0495,0
+CdCl3-,NA,CdCl3-,aq,BZA10,NA,2010-07-03,HKF,cal,-115399,NA,45.15,97.78,63.47,10.8045,18.5994,-1.5605,-3.5479,72.0244,16.8832,0.9378,-1
+CdCl4-2,NA,CdCl4-2,aq,BZA10,NA,2010-07-03,HKF,cal,-145583,NA,50.61,42.52,81.35,13.8329,25.9938,-4.4669,-3.8536,53.6766,5.6267,2.4766,-2
Modified: pkg/CHNOSZ/inst/extdata/adds/SK95.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/adds/SK95.csv 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/inst/extdata/adds/SK95.csv 2022-09-19 09:32:39 UTC (rev 743)
@@ -1,55 +1,55 @@
-name,abbrv,formula,state,ref1,ref2,date,model,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-alanate,NA,C3H6NO2-,aq,SK95,CHNOSZ,2006-09-03,HKF,-74660,-120910,30.25,17.8,61.88,10.6281,17.3648,0.6505,-3.4968,12.685,-4.1859,1.17,-1
-glycinate,NA,C2H4NO2-,aq,SK95,CHNOSZ,2006-09-03,HKF,-75280,-112300,28.48,-6.6,43.77,8.1592,11.7696,1.921,-3.2655,12.9389,-4.1859,1.1975,-1
-Ca(Gly)+,NA,Ca(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-209240,-238629,32.785,59.3,32.6,6.2431,7.4595,2.8241,-3.0873,41.4246,9.0464,0.0543,1
-Ca(Gly)2,NA,Ca(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-285555,-347942,74.749,131,89,13.9371,26.2517,-4.5733,-3.8641,82.6597,23.6485,-0.03,0
-Mg(Gly)+,NA,Mg(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-188490,-225174,6.198,64.2,28.7,5.8466,6.4953,3.1944,-3.0474,48.0086,10.0502,0.4555,1
-Mg(Gly)2,NA,Mg(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-267874,-340003,39.956,140.6,84.7,13.3443,24.8034,-4.0028,-3.8043,88.2942,25.6069,-0.03,0
-Sr(Gly)+,NA,Sr(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-211334,-239307,40.925,53.6,33.3,6.3007,7.6019,2.7652,-3.0932,36.9719,7.8914,-0.0684,1
-Sr(Gly)2,NA,Sr(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-287199,-347420,85.401,119.9,89.8,14.0476,26.5176,-4.6704,-3.8751,76.1763,21.395,-0.03,0
-Ba(Gly)+,NA,Ba(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-211341,-235808,54.327,48.6,38.7,6.9656,9.2295,2.1164,-3.1604,32.1389,6.8602,-0.2709,1
-Ba(Gly)2,NA,Ba(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-287819,-343302,102.94,110.1,95.8,14.8647,28.514,-5.4575,-3.9577,70.3874,19.383,-0.03,0
-Mn(Gly)+,NA,Mn(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-134771,-165803,25,67,33.7,6.4299,7.9186,2.6372,-3.1063,47.0493,10.6185,0.1739,1
-Mn(Gly)2,NA,Mn(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-214101,-278847,64.561,146.1,90.2,14.1002,26.6481,-4.7253,-3.8805,91.4846,26.7157,-0.03,0
-Fe(Gly)+,NA,Fe(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-103038,-135251,20,58,28,5.6774,6.0837,3.3533,-3.0304,42.4593,8.7852,0.2482,1
-Fe(Gly)2,NA,Fe(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-182709,-248527,58.018,128.5,83.9,13.2339,24.5311,-3.8903,-3.793,81.1932,23.1388,-0.03,0
-Ni(Gly)+,NA,Ni(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-94541,-129289,12,49.9,20.4,4.6813,3.6515,4.3097,-2.9299,38.8214,7.1352,0.3686,1
-Ni(Gly)2,NA,Ni(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-176531,-246055,48,112.7,75.4,12.0787,21.7107,-2.7819,-3.6764,71.9311,19.9195,-0.03,0
-Cu(Gly)+,NA,Cu(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-71295,-102408,25,63.4,25.3,5.2864,5.1238,3.7413,-2.9907,44.9395,9.8852,0.1739,1
-Cu(Gly)2,NA,Cu(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-156477,-221770,63,139,80.9,12.8262,23.5338,-3.4944,-3.7518,87.3679,25.285,-0.03,0
-Zn(Gly)+,NA,Zn(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-117818,-151609,18,62.1,25.6,5.3677,5.3226,3.6628,-2.9989,45.1185,9.6102,0.2792,1
-Zn(Gly)2,NA,Zn(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-199139,-267408,55,136.4,81.3,12.8771,23.6625,-3.5537,-3.7571,85.8243,24.7484,-0.03,0
-Pb(Gly)+,NA,Pb(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-88450,-112312,56.918,47.7,35.3,6.4949,8.079,2.5712,-3.1129,31.2483,6.6769,-0.3103,1
-Pb(Gly)2,NA,Pb(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-168353,-222992,106.33,108.3,92.1,14.355,27.2722,-4.9746,-3.9063,69.3582,19.0253,-0.03,0
-Co(Gly)+,NA,Co(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-95195,-129082,15,58.7,25.5,5.3683,5.3273,3.6539,-2.9991,43.5722,8.9227,0.326,1
-Co(Gly)2,NA,Co(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-175957,-243427,55,129.8,81.2,12.8601,23.6197,-3.5341,-3.7553,81.9652,23.407,-0.03,0
-Cd(Gly)+,NA,Cd(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-100236,-132088,27,68.4,35.3,6.6477,8.4525,2.4231,-3.1283,47.5446,10.8935,0.1417,1
-Cd(Gly)2,NA,Cd(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-180576,-246607,65,148.7,92.1,14.355,27.2722,-4.9746,-3.9063,93.0282,27.2523,-0.03,0
-Eu(Gly)+,NA,Eu(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-206629,-234136,47.919,89.8,50.3,8.5841,13.176,0.5767,-3.3236,57.1645,15.2476,-0.1738,1
-Eu(Gly)2,NA,Eu(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-283817,-342929,94.554,190.4,108.7,16.6314,32.8272,-7.1514,-4.136,117.4699,35.7476,-0.03,0
-Ca(Ala)+,NA,Ca(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-208472,-247083,34.555,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
-Ca(Ala)2,NA,Ca(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-284046,-364714,78.835,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
-Mg(Ala)+,NA,Mg(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-185839,-231745,7.968,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
-Mg(Ala)2,NA,Mg(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-262231,-352641,44.042,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
-Sr(Ala)+,NA,Sr(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-210430,-247624,42.695,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
-Sr(Ala)2,NA,Sr(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-285431,-363933,89.487,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
-Ba(Ala)+,NA,Ba(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-210013,-243703,56.097,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
-Ba(Ala)2,NA,Ba(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-285287,-359051,107.026,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
-Mn(Ala)+,NA,Mn(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-133580,-173180,28.965,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
-Mn(Ala)2,NA,Mn(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-212074,-294245,71.52,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
-Fe(Ala)+,NA,Fe(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-103252,-145766,18.058,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
-Fe(Ala)2,NA,Fe(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-182987,-268535,57.246,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
-Ni(Ala)+,NA,Ni(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-93527,-137131,15,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
-Ni(Ala)2,NA,Ni(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-174545,-262972,50,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
-Cu(Ala)+,NA,Cu(C3H6NO2)+,aq,SK95,CHNOSZ,2007-10-12,HKF,-70595,-109970,25,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
-Cu(Ala)2,NA,Cu(C3H6NO2)2,aq,SK95,CHNOSZ,2007-10-12,HKF,-154654,-237360,65,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
-Zn(Ala)+,NA,Zn(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-116613,-160464,17,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
-Zn(Ala)2,NA,Zn(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-197112,-283389,60,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
-Pb(Ala)+,NA,Pb(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-87191,-120275,58.688,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
-Pb(Ala)2,NA,Pb(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-166271,-239191,110.416,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
-Co(Ala)+,NA,Co(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-94099,-136245,20,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
-Co(Ala)2,NA,Co(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-173793,-259272,60,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
-Cd(Ala)+,NA,Cd(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-100082,-141016,29.238,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
-Cd(Ala)2,NA,Cd(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-179940,-263420,71.877,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
-Eu(Ala)+,NA,Eu(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,-205329,-242057,49.689,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
-Eu(Ala)2,NA,Eu(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,-281121,-358514,98.64,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0
+name,abbrv,formula,state,ref1,ref2,date,model,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
+alanate,NA,C3H6NO2-,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-74660,-120910,30.25,17.8,61.88,10.6281,17.3648,0.6505,-3.4968,12.685,-4.1859,1.17,-1
+glycinate,NA,C2H4NO2-,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-75280,-112300,28.48,-6.6,43.77,8.1592,11.7696,1.921,-3.2655,12.9389,-4.1859,1.1975,-1
+Ca(Gly)+,NA,Ca(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-209240,-238629,32.785,59.3,32.6,6.2431,7.4595,2.8241,-3.0873,41.4246,9.0464,0.0543,1
+Ca(Gly)2,NA,Ca(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-285555,-347942,74.749,131,89,13.9371,26.2517,-4.5733,-3.8641,82.6597,23.6485,-0.03,0
+Mg(Gly)+,NA,Mg(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-188490,-225174,6.198,64.2,28.7,5.8466,6.4953,3.1944,-3.0474,48.0086,10.0502,0.4555,1
+Mg(Gly)2,NA,Mg(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-267874,-340003,39.956,140.6,84.7,13.3443,24.8034,-4.0028,-3.8043,88.2942,25.6069,-0.03,0
+Sr(Gly)+,NA,Sr(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-211334,-239307,40.925,53.6,33.3,6.3007,7.6019,2.7652,-3.0932,36.9719,7.8914,-0.0684,1
+Sr(Gly)2,NA,Sr(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-287199,-347420,85.401,119.9,89.8,14.0476,26.5176,-4.6704,-3.8751,76.1763,21.395,-0.03,0
+Ba(Gly)+,NA,Ba(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-211341,-235808,54.327,48.6,38.7,6.9656,9.2295,2.1164,-3.1604,32.1389,6.8602,-0.2709,1
+Ba(Gly)2,NA,Ba(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-287819,-343302,102.94,110.1,95.8,14.8647,28.514,-5.4575,-3.9577,70.3874,19.383,-0.03,0
+Mn(Gly)+,NA,Mn(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-134771,-165803,25,67,33.7,6.4299,7.9186,2.6372,-3.1063,47.0493,10.6185,0.1739,1
+Mn(Gly)2,NA,Mn(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-214101,-278847,64.561,146.1,90.2,14.1002,26.6481,-4.7253,-3.8805,91.4846,26.7157,-0.03,0
+Fe(Gly)+,NA,Fe(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-103038,-135251,20,58,28,5.6774,6.0837,3.3533,-3.0304,42.4593,8.7852,0.2482,1
+Fe(Gly)2,NA,Fe(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-182709,-248527,58.018,128.5,83.9,13.2339,24.5311,-3.8903,-3.793,81.1932,23.1388,-0.03,0
+Ni(Gly)+,NA,Ni(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-94541,-129289,12,49.9,20.4,4.6813,3.6515,4.3097,-2.9299,38.8214,7.1352,0.3686,1
+Ni(Gly)2,NA,Ni(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-176531,-246055,48,112.7,75.4,12.0787,21.7107,-2.7819,-3.6764,71.9311,19.9195,-0.03,0
+Cu(Gly)+,NA,Cu(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-71295,-102408,25,63.4,25.3,5.2864,5.1238,3.7413,-2.9907,44.9395,9.8852,0.1739,1
+Cu(Gly)2,NA,Cu(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-156477,-221770,63,139,80.9,12.8262,23.5338,-3.4944,-3.7518,87.3679,25.285,-0.03,0
+Zn(Gly)+,NA,Zn(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-117818,-151609,18,62.1,25.6,5.3677,5.3226,3.6628,-2.9989,45.1185,9.6102,0.2792,1
+Zn(Gly)2,NA,Zn(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-199139,-267408,55,136.4,81.3,12.8771,23.6625,-3.5537,-3.7571,85.8243,24.7484,-0.03,0
+Pb(Gly)+,NA,Pb(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-88450,-112312,56.918,47.7,35.3,6.4949,8.079,2.5712,-3.1129,31.2483,6.6769,-0.3103,1
+Pb(Gly)2,NA,Pb(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-168353,-222992,106.33,108.3,92.1,14.355,27.2722,-4.9746,-3.9063,69.3582,19.0253,-0.03,0
+Co(Gly)+,NA,Co(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-95195,-129082,15,58.7,25.5,5.3683,5.3273,3.6539,-2.9991,43.5722,8.9227,0.326,1
+Co(Gly)2,NA,Co(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-175957,-243427,55,129.8,81.2,12.8601,23.6197,-3.5341,-3.7553,81.9652,23.407,-0.03,0
+Cd(Gly)+,NA,Cd(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-100236,-132088,27,68.4,35.3,6.6477,8.4525,2.4231,-3.1283,47.5446,10.8935,0.1417,1
+Cd(Gly)2,NA,Cd(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-180576,-246607,65,148.7,92.1,14.355,27.2722,-4.9746,-3.9063,93.0282,27.2523,-0.03,0
+Eu(Gly)+,NA,Eu(C2H4NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-206629,-234136,47.919,89.8,50.3,8.5841,13.176,0.5767,-3.3236,57.1645,15.2476,-0.1738,1
+Eu(Gly)2,NA,Eu(C2H4NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-283817,-342929,94.554,190.4,108.7,16.6314,32.8272,-7.1514,-4.136,117.4699,35.7476,-0.03,0
+Ca(Ala)+,NA,Ca(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-208472,-247083,34.555,104.6,50.7,8.7124,13.4888,0.454,-3.3365,67.7227,18.2713,0.0279,1
+Ca(Ala)2,NA,Ca(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-284046,-364714,78.835,239.1,127.3,19.1765,39.0448,-9.6021,-4.393,146.0369,45.6768,-0.03,0
+Mg(Ala)+,NA,Mg(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-185839,-231745,7.968,109.5,46.8,8.3169,12.5282,0.821,-3.2968,74.3351,19.275,0.4322,1
+Mg(Ala)2,NA,Mg(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-262231,-352641,44.042,248.8,123,18.5836,37.5967,-9.0318,-4.3331,151.6713,47.6352,-0.03,0
+Sr(Ala)+,NA,Sr(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-210430,-247624,42.695,98.9,51.4,8.77,13.6312,0.3947,-3.3424,63.2691,17.1163,-0.0948,1
+Sr(Ala)2,NA,Sr(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-285431,-363933,89.487,228.1,128.1,19.2869,39.3109,-9.699,-4.404,139.5534,43.4233,-0.03,0
+Ba(Ala)+,NA,Ba(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-210013,-243703,56.097,93.7,56.8,9.4348,15.2528,-0.2391,-3.4095,58.4325,16.085,-0.2977,1
+Ba(Ala)2,NA,Ba(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-285287,-359051,107.026,218.2,134.1,20.104,41.3073,-10.4865,-4.4865,133.7647,41.4112,-0.03,0
+Mn(Ala)+,NA,Mn(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-133580,-173180,28.965,112.3,51.8,8.8873,13.9167,0.2842,-3.3542,73.0237,19.8433,0.1124,1
+Mn(Ala)2,NA,Mn(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-212074,-294245,71.52,254.2,128.5,19.3395,39.4414,-9.7539,-4.4094,154.8617,48.744,-0.03,0
+Fe(Ala)+,NA,Fe(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-103252,-145766,18.058,103.3,46.1,8.1661,12.1558,0.976,-3.2814,69.2856,18.01,0.2792,1
+Fe(Ala)2,NA,Fe(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-182987,-268535,57.246,236.6,122.2,18.4732,37.3244,-8.9189,-4.3219,144.5703,45.1671,-0.03,0
+Ni(Ala)+,NA,Ni(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-93527,-137131,15,95.2,38.5,7.1451,9.664,1.9536,-3.1784,64.9703,16.36,0.326,1
+Ni(Ala)2,NA,Ni(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-174545,-262972,50,220.8,113.8,17.318,34.504,-7.8105,-4.2053,135.3083,41.9478,-0.03,0
+Cu(Ala)+,NA,Cu(C3H6NO2)+,aq,SK95,CHNOSZ,2007-10-12,HKF,cal,-70595,-109970,25,108.7,43.4,7.7387,11.1165,1.3762,-3.2385,70.7759,19.11,0.0974,1
+Cu(Ala)2,NA,Cu(C3H6NO2)2,aq,SK95,CHNOSZ,2007-10-12,HKF,cal,-154654,-237360,65,247.2,119.2,18.0655,36.3271,-8.523,-4.2807,150.7452,47.3132,-0.03,0
+Zn(Ala)+,NA,Zn(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-116613,-160464,17,107.4,43.8,7.8514,11.3891,1.2746,-3.2497,71.8106,18.835,0.2956,1
+Zn(Ala)2,NA,Zn(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-197112,-283389,60,244.5,119.6,18.1164,36.4558,-8.5823,-4.286,149.2015,46.7767,-0.03,0
+Pb(Ala)+,NA,Pb(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-87191,-120275,58.688,93,53.4,8.964,14.1088,0.1992,-3.3622,57.5413,15.9017,-0.3372,1
+Pb(Ala)2,NA,Pb(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-166271,-239191,110.416,216.4,130.4,19.5944,40.0653,-10.0034,-4.4352,132.7356,41.0535,-0.03,0
+Co(Ala)+,NA,Co(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-94099,-136245,20,104,43.6,7.8202,11.3148,1.299,-3.2467,69.3955,18.1475,0.2482,1
+Co(Ala)2,NA,Co(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-173793,-259272,60,238,119.4,18.0995,36.4127,-8.5626,-4.2842,145.3423,45.4353,-0.03,0
+Cd(Ala)+,NA,Cd(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-100082,-141016,29.238,113.7,53.4,9.1151,14.4742,0.063,-3.3773,73.7914,20.1183,0.1098,1
+Cd(Ala)2,NA,Cd(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-179940,-263420,71.877,256.8,130.4,19.5944,40.0653,-10.0034,-4.4352,156.4053,49.2806,-0.03,0
+Eu(Ala)+,NA,Eu(C3H6NO2)+,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-205329,-242057,49.689,135,68.4,11.0532,19.2058,-1.7947,-3.5729,83.4588,24.4724,-0.2006,1
+Eu(Ala)2,NA,Eu(C3H6NO2)2,aq,SK95,CHNOSZ,2006-09-03,HKF,cal,-281121,-358514,98.64,298.5,147,21.8707,45.6205,-12.1799,-4.6649,180.847,57.7759,-0.03,0
Modified: pkg/CHNOSZ/inst/tinytest/test-util.data.R
===================================================================
--- pkg/CHNOSZ/inst/tinytest/test-util.data.R 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/inst/tinytest/test-util.data.R 2022-09-19 09:32:39 UTC (rev 743)
@@ -53,14 +53,6 @@
# the order isn't guaranteed ... just make sure they're all there
expect_true(all(newdat$name %in% thermo()$OBIGT$name[isp]), info = info)
-info <- "add.OBIGT() is backwards compatible for a file that doesn't have an E_units column"
-# test added 20190529
-file <- system.file("extdata/adds/BZA10.csv", package = "CHNOSZ")
-rc <- read.csv(file)
-expect_false("E_units" %in% colnames(rc), info = info)
-inew <- add.OBIGT(file)
-expect_true(unique(info(inew, check.it = FALSE)$E_units) == "cal", info = info)
-
info <- "add.OBIGT() gives an error for an incompatible file"
# test added 20191210
file <- system.file("extdata/Berman/Ber88_1988.csv", package = "CHNOSZ")
Modified: pkg/CHNOSZ/man/add.OBIGT.Rd
===================================================================
--- pkg/CHNOSZ/man/add.OBIGT.Rd 2022-09-19 04:03:34 UTC (rev 742)
+++ pkg/CHNOSZ/man/add.OBIGT.Rd 2022-09-19 09:32:39 UTC (rev 743)
@@ -25,7 +25,7 @@
\code{\link{add.OBIGT}} is used to update the thermodynamic database (\code{\link{thermo}$OBIGT}) in the running session.
The format (column names) of the specified file must be the same as the \code{extdata/OBIGT/*.csv} files provided with CHNOSZ.
-However, for backwards compatibility, the \code{E_units} column of the input can be missing; then, it is assigned a value of \samp{cal} (this differs from the default setting for \code{\link{E.units}}, which applies to the thermodynamic properties output by \code{\link{subcrt}} and not to database entries).
+Note that this includes both the \code{E_units} and \code{model} columns, which were added in versions 1.3.3 and 2.0.0.
\code{file} is first matched against the names of files in the \code{extdata/OBIGT} directory packaged with CHNOSZ.
In this case, the file suffixes are removed, so \samp{DEW}, \samp{organic_aq}, and \samp{organic_cr} are valid names.
More information about the CHNOSZ-commits
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