[CHNOSZ-commits] r678 - in pkg/CHNOSZ: . demo inst inst/extdata/OBIGT

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon May 17 12:42:12 CEST 2021 

Author: jedick
Date: 2021-05-17 12:42:12 +0200 (Mon, 17 May 2021)
New Revision: 678

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/demo/Pourbaix.R
   pkg/CHNOSZ/inst/CITATION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
   pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
Log:
Move Ar, Xe, CH4, and CO2 from organic_aq.csv to inorganic_aq.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2021-05-11 23:20:26 UTC (rev 677)
+++ pkg/CHNOSZ/DESCRIPTION	2021-05-17 10:42:12 UTC (rev 678)
@@ -1,6 +1,6 @@
-Date: 2021-05-12
+Date: 2021-05-17
 Package: CHNOSZ
-Version: 1.4.1-4
+Version: 1.4.1-5
 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/demo/Pourbaix.R
===================================================================
--- pkg/CHNOSZ/demo/Pourbaix.R	2021-05-11 23:20:26 UTC (rev 677)
+++ pkg/CHNOSZ/demo/Pourbaix.R	2021-05-17 10:42:12 UTC (rev 678)
@@ -4,14 +4,16 @@
 # 20210301 jmd first version
 
 library(CHNOSZ)
+# Load OBIGT database without organic species
+# (speeds up and reduces memory needed for C diagram)
+OBIGT(no.organics = TRUE)
 
 ### PARAMETERS (to be changed by the user) ###
 
 # Choose an element
-# Some mostly working ones: Fe, Cu, Au, Rh, Mn
+# Some mostly working ones: Fe, Cu, Au, Rh, Mn, C
 # Incomplete: Al (no native metal), Ni, ...
-# Not working: C, Cr, ...
-#  (C gives lots of organic species, probably getting an NA affinity somewhere)
+# Not working: Cr, ...
 #  (Cr has no solids in OBIGT)
 element <- "Fe"
 

Modified: pkg/CHNOSZ/inst/CITATION
===================================================================
--- pkg/CHNOSZ/inst/CITATION	2021-05-11 23:20:26 UTC (rev 677)
+++ pkg/CHNOSZ/inst/CITATION	2021-05-17 10:42:12 UTC (rev 678)
@@ -2,17 +2,31 @@
          title = "CHNOSZ: Thermodynamic calculations and diagrams for geochemistry",
          author = person(given = c("Jeffrey", "M."), family = "Dick", email="jeff at chnosz.net"),
          journal = "Frontiers in Earth Science",
-	 year = "2019",
+         year = "2019",
          volume = "7",
          number = "",
          pages = "180",
          doi = "10.3389/feart.2019.00180"
-	 )
+)
 
 bibentry(bibtype = "Article",
          title = "Diagrams with multiple metals in CHNOSZ",
          author = person(given = c("Jeffrey", "M."), family = "Dick", email="jeff at chnosz.net"),
          journal = "Applied Computing and Geosciences",
-	 year = "2021",
+         year = "2021",
+         volume = "10",
+         number = "",
+         pages = "100059",
          doi = "10.1016/j.acags.2021.100059"
-	 )
+)
+
+bibentry(bibtype = "Article",
+         title = "Calculation of the relative metastabilities of proteins using the CHNOSZ software package",
+         author = person(given = c("Jeffrey", "M."), family = "Dick", email="jmdick at asu.edu"),
+         journal = "Geochemical Transactions",
+         year = "2008",
+         volume = "9",
+         number = "",
+         pages = "10",
+         doi = "10.1186/1467-4866-9-10"
+)

Modified: pkg/CHNOSZ/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2021-05-11 23:20:26 UTC (rev 677)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2021-05-17 10:42:12 UTC (rev 678)
@@ -10,6 +10,18 @@
 \newcommand{\s}{\ifelse{latex}{\eqn{_{#1}}}{\ifelse{html}{\out{<sub>#1</sub>}}{#1}}}
 \newcommand{\S}{\ifelse{latex}{\eqn{^{#1}}}{\ifelse{html}{\out{<sup>#1</sup>}}{^#1}}}
 
+\section{Changes in CHNOSZ version 1.4.1-5 (2021-05-17)}{
+
+  \subsection{OBIGT DATABASE}{
+    \itemize{
+
+      \item Move Ar, Xe, CH\s{4}, and CO\s{2} from organic_aq.csv to inorganic_aq.csv.
+      
+    }
+  }
+
+}
+
 \section{Changes in CHNOSZ version 1.4.1 (2021-04-08)}{
 
   \subsection{NEW FEATURES}{

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv	2021-05-11 23:20:26 UTC (rev 677)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/inorganic_aq.csv	2021-05-17 10:42:12 UTC (rev 678)
@@ -700,6 +700,10 @@
 Rh(SO4)3-3,Rh(SO4)3-3,Rh(SO4)3-3,aq,SS98a,NA,1995-03-30,cal,-483700,-583100,37.9,-73.3,37.5,8.3237,12.5416,0.8232,-3.2974,2.2248,-17.9739,4.2376,-3
 RhOH+2,Rh(OH)+2,Rh(OH)+2,aq,SS98a,NA,1995-07-13,cal,-820,-14620,-32.5,-0.1,-0.3,2.247,-2.2946,6.6503,-2.684,20.365,-3.0549,1.5475,2
 RhO+,RhO+,RhO+,aq,SS98a,NA,1994-07-25,cal,3140,-10010,-18.7,-39.5,1.9,2.3067,-2.1515,6.6002,-2.69,-9.3049,-11.0806,0.8334,1
+Ar,Ar,Ar,aq,PS01,NA,2000-10-04,cal,3890,-2880,14.3,52.82,32.6,11.71,-2.39,-44.93,1.91,27.96,9.56,-0.46,0
+Xe,Xe,Xe,aq,PS01,NA,2000-10-04,cal,3215,-4540,14.5,64.77,42.5,18.4,-2.39,-59.03,1.43,35.85,13.86,-0.39,0
+CH4,NA,CH4,aq,PS01,NA,2000-10-04,cal,-8140,-20930,21,60.23,36,17.69,-15.3,-67.88,11.47,40.87,6.45,-0.4,0
+CO2,NA,CO2,aq,PS01,NA,2005-08-18,cal,-92250,-98900,28.1,51.86,33.5,15.2964,-10.0382,-55.4493,7.4092,36.8069,3.5851,-0.3107,0
 CF4,NA,CF4,aq,SSW01,NA,2006-09-01,cal,-202700,-224680,32.4,105.4,0,0,0,0,0,51.2936,28.0572,-0.3282,0
 SF6,NA,SF6,aq,SSW01,NA,2006-09-01,cal,-259240,-293780,37.2,146.4,0,0,0,0,0,61.295,40.7143,-0.2601,0
 NF3,NA,NF3,aq,SSW01,NA,2006-09-01,cal,-15660,-33515,35.7,82.8,0,0,0,0,0,43.4774,18.2721,-0.2406,0

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv	2021-05-11 23:20:26 UTC (rev 677)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/organic_aq.csv	2021-05-17 10:42:12 UTC (rev 678)
@@ -1,5 +1,4 @@
 name,abbrv,formula,state,ref1,ref2,date,E_units,G,H,S,Cp,V,a1.a,a2.b,a3.c,a4.d,c1.e,c2.f,omega.lambda,z.T
-CH4,NA,CH4,aq,PS01,NA,2000-10-04,cal,-8140,-20930,21,60.23,36,17.69,-15.3,-67.88,11.47,40.87,6.45,-0.4,0
 ethane,NA,C2H6,aq,SH90,NA,1987-08-31,cal,-3886,-24650,26.81,88.3,51.3,8.634,13.3011,0.5205,-3.3288,54.1755,14.9521,-0.406,0
 propane,NA,C3H8,aq,SH90,NA,1987-08-31,cal,-1963,-30490,33.37,110.6,67,10.7625,18.4948,-1.5133,-3.5435,66.3294,19.4946,-0.5053,0
 butane,NA,C4H10,aq,SH90,NA,1993-01-15,cal,36,-36230,40.02,133.9,82.8,12.8905,23.696,-3.5683,-3.7585,79.0569,24.2408,-0.6061,0
@@ -636,10 +635,7 @@
 Sr(Adip),NA,SrC6H8O4,aq,PSK99,NA,2006-08-24,cal,-296914,-356443,44.1,46.2,0,0,0,0,0,30.5019,6.3763,-0.3278,0
 Cr(Adip),NA,CrC6H8O4,aq,PSK99,NA,2006-08-24,cal,-201745,-262618,32.7,49.1,0,0,0,0,0,33.6447,6.9671,-0.1552,0
 cyclohexane,CYHEX,C6H12,aq,PS01,NA,2011-02-19,cal,10780,-37400,34,122.904,87,39.67,-4.3,-120.7,2.39,90.82,18.64,-0.39,0
-Ar,Ar,Ar,aq,PS01,NA,2000-10-04,cal,3890,-2880,14.3,52.82,32.6,11.71,-2.39,-44.93,1.91,27.96,9.56,-0.46,0
 benzene,NA,C6H6,aq,PS01,NA,2000-10-04,cal,32010,12220,35.6,88.43,83,36.09,-15.77,-115.92,10.76,66.92,9.8,-0.25,0
-CO2,NA,CO2,aq,PS01,NA,2005-08-18,cal,-92250,-98900,28.1,51.86,33.5,15.2964,-10.0382,-55.4493,7.4092,36.8069,3.5851,-0.3107,0
-Xe,Xe,Xe,aq,PS01,NA,2000-10-04,cal,3215,-4540,14.5,64.77,42.5,18.4,-2.39,-59.03,1.43,35.85,13.86,-0.39,0
 perchloroethylene,PCE,C2Cl4,aq,HS99,NA,2012-05-01,cal,7483,-12995,40.7,160,91.1,14.1804,26.8436,-4.8012,-3.8886,98.5546,29.5574,-0.15,0
 trichloroethylene,TCE,C2HCl3,aq,HS99,NA,2012-05-01,cal,6061,-11852,38.26,135,81.3,12.8394,23.5678,-3.5109,-3.7532,83.9031,24.4649,-0.15,0
 "1,1-dichloroethylene","1,1-DCE",C2H2Cl2,aq,HS99,NA,2012-05-01,cal,7726,-6739,38.78,95,68.2,11.0468,19.1914,-1.7922,-3.5723,60.4606,16.3169,-0.15,0

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