[CHNOSZ-commits] r69 - in pkg/CHNOSZ: . R data inst inst/extdata/thermo man

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Tue Dec 9 06:05:54 CET 2014 

Author: jedick
Date: 2014-12-09 06:05:51 +0100 (Tue, 09 Dec 2014)
New Revision: 69

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/transfer.R
   pkg/CHNOSZ/data/OBIGT.csv
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv
   pkg/CHNOSZ/man/CHNOSZ-package.Rd
   pkg/CHNOSZ/man/data.Rd
   pkg/CHNOSZ/man/transfer.Rd
Log:
move H4SiO4 to OBIGT-2.csv


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/DESCRIPTION	2014-12-09 05:05:51 UTC (rev 69)
@@ -1,6 +1,6 @@
-Date: 2014-12-08
+Date: 2014-12-09
 Package: CHNOSZ
-Version: 1.0.3-6
+Version: 1.0.3-7
 Title: Chemical Thermodynamics and Activity Diagrams
 Author: Jeffrey Dick
 Maintainer: Jeffrey Dick <j3ffdick at gmail.com>

Modified: pkg/CHNOSZ/R/transfer.R
===================================================================
--- pkg/CHNOSZ/R/transfer.R	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/R/transfer.R	2014-12-09 05:05:51 UTC (rev 69)
@@ -807,7 +807,8 @@
   # setup conditions for feldspar reaction
   #basis(c('Al+3','SiO2','K+','H2O','H+','O2'))
   basis(delete=TRUE)
-  # SLS89 use H4SiO4 instead of SiO2
+  # SLS89 use H4SiO4 instead of SiO2 - use the secondary database
+  add.obigt()
   basis(c('Al+3','H4SiO4','K+','H2O','H+','O2'))
   # some of SLS89's initial conditions
   basis(c('K+','H4SiO4'),c(-6,-6))

Modified: pkg/CHNOSZ/data/OBIGT.csv
===================================================================
--- pkg/CHNOSZ/data/OBIGT.csv	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/data/OBIGT.csv	2014-12-09 05:05:51 UTC (rev 69)
@@ -1768,8 +1768,6 @@
 "dibutyl sulfide",NA,C8H18S,aq,Sch10,NA,03.Jul.10,13260,-51810,81.4,195,162.7,23.7393,57.9427,-33.671,-5.1744,177.4725,5.2072,-0.7624,0
 "dipentyl sulfide",NA,C10H22S,aq,Sch10,NA,03.Jul.10,17360,-63150,94.8,238,194.3,28.0757,67.7711,-35.9048,-5.5807,213.8806,8.5956,-0.7302,0
 "dihexyl sulfide",NA,C12H26S,aq,Sch10,NA,03.Jul.10,21460,-74490,108.2,280,225.9,32.412,77.5996,-38.1385,-5.987,249.442,11.9085,-0.698,0
-Ti(OH)4,NA,Ti(OH)4,aq,Ste01,NA,31.Aug.06,-313690.248565966,-361331.022944551,5.23900573613767,48.4942638623327,40.6,7.36687380497132,10.210086042065,1.15296367112811,-3.20100382409178,51.2762906309751,-1.27652963671128,0.01498565965583,0
-H4SiO4,NA,H4SiO4,aq,Ste01,NA,31.Aug.06,-312919.933078394,-348676.147227533,45.1003824091778,15.0095602294455,52.3,18.7299235181644,-21.2600382409178,18.6199808795411,-1.20004780114723,58.0305927342256,-20.789913957935,0.08690248565966,0
 Br2,bromine,Br2,aq,WEP+82,NA,27.Apr.11,939.3,-619,31.19,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 I2,iodine,I2,aq,WEP+82,NA,27.Apr.11,3919.7,5401.5,32.79,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 2-methylpropane,NA,C4H10,aq,CGM+81,NA,7.Aug.11,NA,NA,NA,-11.38,NA,NA,NA,NA,NA,NA,NA,NA,NA

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/inst/NEWS	2014-12-09 05:05:51 UTC (rev 69)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.3-6 (2014-12-08)
+CHANGES IN CHNOSZ 1.0.3-7 (2014-12-09)
 --------------------------------------
 
 - Add files with average amino acid compositions of proteins from Bison
@@ -15,6 +15,10 @@
   labels and indices of those species in predominance diagrams,
   including when the labels aren't plotted (by setting names=FALSE).
 
+- Move aqueous Ti(OH)4 and H4SiO4 to OBIGT-2.csv.
+
+- Add warning about data and examples to CHNOSZ-package.Rd.
+
 CHANGES IN CHNOSZ 1.0.3 (2014-01-12)
 ------------------------------------
 

Modified: pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/inst/extdata/thermo/OBIGT-2.csv	2014-12-09 05:05:51 UTC (rev 69)
@@ -248,6 +248,8 @@
 TmCl2+,NA,TmCl2+,aq,MWW09,NA,03.Jul.10,-223290,NA,-20.2,4.66,1.26,2.2586,-2.2666,6.6409,-2.6853,16.6521,-2.0854,0.85,1
 YbCl2+,NA,YbCl2+,aq,MWW09,NA,03.Jul.10,-216360,NA,-19.22,-4.55,-0.6,1.9985,-2.9017,6.8906,-2.659,11.1191,-3.9614,0.8351,1
 LuCl2+,NA,LuCl2+,aq,MWW09,NA,03.Jul.10,-222750,NA,-30.31,11.26,-1.23,1.9757,-2.9572,6.9124,-2.6567,21.9175,-0.7409,1.0031,1
+Ti(OH)4,NA,Ti(OH)4,aq,Ste01,NA,31.Aug.06,-313690.248565966,-361331.022944551,5.23900573613767,48.4942638623327,40.6,7.36687380497132,10.210086042065,1.15296367112811,-3.20100382409178,51.2762906309751,-1.27652963671128,0.0149856596558317,0
+H4SiO4,NA,H4SiO4,aq,Ste01,NA,31.Aug.06,-312919.933078394,-348676.147227533,45.1003824091778,15.0095602294455,52.3,18.7299235181644,-21.2600382409178,18.6199808795411,-1.20004780114723,58.0305927342256,-20.789913957935,0.0869024856596558,0
 arsenolite,NA,As2O3,cr,PGS+96,NA,25.Aug.06,-137640,-156930,25.67,23.15,51.12,20.9,17.73,-2.7,0,0,0,0,548
 claudetite,NA,As2O3,cr,PGS+96,NA,25.Aug.06,-137730,-156600,27.09,23.19,47.26,23.86,10.74,-3.44,0,0,0,0,588
 orpiment,NA,As2S3,cr,PGS+96,NA,25.Aug.06,-20550,-20700,39.1,27.53,70.5,22.73,13.82,0.605,0,0,0,0,580

Modified: pkg/CHNOSZ/man/CHNOSZ-package.Rd
===================================================================
--- pkg/CHNOSZ/man/CHNOSZ-package.Rd	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/man/CHNOSZ-package.Rd	2014-12-09 05:05:51 UTC (rev 69)
@@ -6,8 +6,21 @@
   CHNOSZ is a package for thermodynamic calculations, primarily with applications in geochemistry and biochemistry. It can be used to calculate the standard molal thermodynamic properties and chemical affinities of reactions relevant to geobiochemical processes, and to visualize the equilibrium activities of species on chemical speciation and predominance diagrams. The package can be used interactively and in batch mode, through the use of R source files containing a sequence of commands. The major features of the package are outlined below, with links to specific help topics in this document, which constitutes the primary technical description of the package. If you are a new user, the \sQuote{anintro} vignette (An introduction to CHNOSZ) may offer a more comfortable way to get started with using the package.
 }
 
-\details{
+\section{Warning}{
+All thermodynamic data and examples are provided on an as-is basis.
+It is up to you to check not only the accuracy of the data, but also the \emph{suitability of the data for your problem}.
+By combining data taken from different sources, it is possible to build an inconsistent and/or nonsensical calculation.
+An attempt has been made to provide a primary database (OBIGT.csv) that is internally consistent, but no guarantee can be made.
+Where possible, data with known or suspected inconsistencies have been placed into a secondary database (OBIGT-2.csv) that should be regarded as experimental.
+If there is any doubt about the accuracy or suitability of data for a particular problem, PLEASE consult the primary sources (see \code{\link{browse.refs}}).
+Do not assume that by adding any species to your calculation (or to any of the examples), you will necessarily obtain a reasonable answer.
+Do not assume that the examples are correct, either by themselves, or for your problem.
+As with the data, PLEASE compare the construction and output of the examples to the primary sources, cited in the help page reference list.
+Examples without a reference (and some with references) demonstrate experimental features of CHNOSZ.
+}
 
+\section{Overview}{
+
   Major features in CHNOSZ:
 
 \itemize{

Modified: pkg/CHNOSZ/man/data.Rd
===================================================================
--- pkg/CHNOSZ/man/data.Rd	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/man/data.Rd	2014-12-09 05:05:51 UTC (rev 69)
@@ -10,6 +10,8 @@
 \alias{buffers}
 \title{Thermodynamic Database and System Definition}
 \description{
+
+  Please read the important Warning at \code{\link{CHNOSZ-package}}.
  
   The core data files provided with CHNOSZ are in the \code{data} directory of the package. These \code{*.csv} files are used to build the \code{thermo} data object on loading the package. Additional (extra) data files, supporting the examples and vignettes, are documented separately at \code{\link{extdata}}. 
 

Modified: pkg/CHNOSZ/man/transfer.Rd
===================================================================
--- pkg/CHNOSZ/man/transfer.Rd	2014-12-08 14:23:52 UTC (rev 68)
+++ pkg/CHNOSZ/man/transfer.Rd	2014-12-09 05:05:51 UTC (rev 69)
@@ -59,6 +59,10 @@
 
 }
 
+\section{Warning}{
+  \code{feldspar} loads the secondary database (using \code{\link{add.obigt}}); after using this function use \code{data(thermo)} to restore the primary database.
+}
+
 \value{
   \code{transfer} returns a list containing information about the conditions at each step: \code{basis}, data frame of the logarithms of activities of basis species, \code{species}, data frame of the logarithms of activities (moles for solids) of species, \code{alphas}, numeric vector of the values of the destruction exponent, \code{dmodes}, character vector of the destruction mode, \code{istables}, numeric vector of the index of the most stable product, \code{myaffs}, list of the affinities of the formation reactions of species, \code{didwork}, logical vector indicating whether the steps succeeded or failed.
 }
@@ -67,6 +71,8 @@
 \examples{\dontshow{data(thermo)}
 \donttest{## react potassium feldspar in a closed system
 ## after Steinmann et al., 1994 and Helgeson et al., 1969
+# load the secondary database to use H4SiO4
+add.obigt()
 basis(c("Al+3", "H4SiO4", "K+", "H2O", "H+", "O2"), c(0, -6, -6, 0, 0, 0))
 species(c("k-feldspar", "muscovite", "pyrophyllite", "kaolinite", "gibbsite"))
 a <- affinity(H4SiO4=c(-6, -2), "K+"=c(-3, 8))
@@ -78,6 +84,8 @@
 draw.transfer(tr)
 # reset the plot layout
 layout(matrix(1))
+# restore the primary database
+data(thermo)
 
 ## can also run the calculation above with
 #feldspar("closed")

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