[CHNOSZ-commits] r317 - in pkg/CHNOSZ: . R inst inst/extdata/OBIGT

[noreply at r-forge.r-project.org]

Author: jedick
Date: 2018-04-29 10:08:08 +0200 (Sun, 29 Apr 2018)
New Revision: 317

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/R/basis.R
   pkg/CHNOSZ/inst/NEWS
   pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
Log:
change abbreviation of grossular to Grs


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION	2018-04-20 14:45:18 UTC (rev 316)
+++ pkg/CHNOSZ/DESCRIPTION	2018-04-29 08:08:08 UTC (rev 317)
@@ -1,6 +1,6 @@
-Date: 2018-04-20
+Date: 2018-04-29
 Package: CHNOSZ
-Version: 1.1.3-24
+Version: 1.1.3-25
 Title: Thermodynamic Calculations and Diagrams for Geochemistry
 Authors at R: c(
     person("Jeffrey", "Dick", , "j3ffdick at gmail.com", role = c("aut", "cre"),
@@ -27,9 +27,10 @@
   (Sverjensky et al., 2014 <doi:10.1016/j.gca.2013.12.019>) and estimates of parameters in the
   extended Debye-Hückel equation (Manning et al., 2013 <doi:10.2138/rmg.2013.75.5>)
   to calculate standard-state properties and activity coefficients for given ionic strength at high
-  pressure (to 60 kb). Functions are provided to define a system using basis species, automatically
-  balance reactions, calculate the chemical affinities of formation reactions for selected species,
-  calculate equilibrium activities, and plot the results on chemical activity diagrams.
+  pressure (to 60 kb). Functions are provided to calculate standard-state properties of species and
+  reactions, define the basis species of a chemical system, automatically balance reactions, calculate
+  the chemical affinities of formation reactions for selected species, calculate the equilibrium
+  activities of those species, and plot the results on chemical activity diagrams.
 Encoding: UTF-8
 License: GPL (>= 2)
 BuildResaveData: no

Modified: pkg/CHNOSZ/R/basis.R
===================================================================
--- pkg/CHNOSZ/R/basis.R	2018-04-20 14:45:18 UTC (rev 316)
+++ pkg/CHNOSZ/R/basis.R	2018-04-29 08:08:08 UTC (rev 317)
@@ -154,7 +154,7 @@
           bufmakeup <- makeup(ispecies)
           inbasis <- names(bufmakeup) %in% colnames(basis()) 
           if(FALSE %in% inbasis) {
-            stop(paste("the elements '",c2s(rownames(bufmakeup)[!inbasis]),
+            stop(paste("the elements '",c2s(names(bufmakeup)[!inbasis]),
               "' of species '",thermo$buffers$species[ibuff[k]],"' in buffer '",state[i],
               "' are not in the basis\n",sep=""))
           }

Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS	2018-04-20 14:45:18 UTC (rev 316)
+++ pkg/CHNOSZ/inst/NEWS	2018-04-29 08:08:08 UTC (rev 317)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.1.3-21 (2018-03-31)
+CHANGES IN CHNOSZ 1.1.3-25 (2018-04-29)
 ---------------------------------------
 
 THERMODYNAMIC DATA
@@ -43,6 +43,8 @@
   equation as d0 .. d4, rename "d5" (constant that scales disordering
   enthalpy to volume) to "Vad" (notation used in Theriak-Domino manual).
 
+- Change abbreviation of grossular to Grs.
+
 OTHER CHANGES
 
 - Lines in 1-D diagram()s can optionally be drawn as splines using the

Modified: pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv	2018-04-20 14:45:18 UTC (rev 316)
+++ pkg/CHNOSZ/inst/extdata/OBIGT/Berman_cr.csv	2018-04-29 08:08:08 UTC (rev 317)
@@ -28,7 +28,7 @@
 ferrosilite,Fsl,SiFeO3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 forsterite,Fo,Mg2SiO4,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 gehlenite,Ge,Al2Ca2SiO7,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
-grossular,Gr,Ca3Al2Si3O12,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
+grossular,Grs,Ca3Al2Si3O12,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 hematite,Hm,Fe2O3,cr,Ber88,NA,01.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 ilmenite,Ilm,FeTiO3,cr,Ber88,Ber90.1,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA
 jadeite,Jd,NaAlSi2O6,cr,Ber88,SHD91,03.Oct.17,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA