[CHNOSZ-commits] r756 - in pkg/CHNOSZ: . inst inst/extdata/thermo man

Sun Nov 27 12:43:35 CET 2022

Author: jedick
Date: 2022-11-27 12:43:35 +0100 (Sun, 27 Nov 2022)
New Revision: 756

Modified:
   pkg/CHNOSZ/DESCRIPTION
   pkg/CHNOSZ/inst/NEWS.Rd
   pkg/CHNOSZ/inst/extdata/thermo/opt.csv
   pkg/CHNOSZ/man/makeup.Rd
   pkg/CHNOSZ/man/subcrt.Rd
   pkg/CHNOSZ/man/thermo.Rd
Log:
Remove unused 'cutoff' value in thermo()$opt


Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================

--- pkg/CHNOSZ/DESCRIPTION	2022-11-25 10:01:43 UTC (rev 755)
+++ pkg/CHNOSZ/DESCRIPTION	2022-11-27 11:43:35 UTC (rev 756)
@@ -1,6 +1,6 @@
-Date: 2022-11-25
+Date: 2022-11-27
 Package: CHNOSZ
-Version: 1.9.9-47
+Version: 1.9.9-48
 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/inst/NEWS.Rd
===================================================================
--- pkg/CHNOSZ/inst/NEWS.Rd	2022-11-25 10:01:43 UTC (rev 755)
+++ pkg/CHNOSZ/inst/NEWS.Rd	2022-11-27 11:43:35 UTC (rev 756)
@@ -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 1.9.9-47 (2022-11-25)}{
+\section{Changes in CHNOSZ version 1.9.9-48 (2022-11-27)}{
 
   \subsection{MAJOR USER-VISIBLE CHANGES}{
     \itemize{
@@ -203,6 +203,8 @@
 
       \item \code{NaCl()} now works with \code{mtot = 0}.
 
+      \item Remove unused \samp{cutoff} value in \code{thermo()$opt}.
+
     }
   }
 

Modified: pkg/CHNOSZ/inst/extdata/thermo/opt.csv
===================================================================
--- pkg/CHNOSZ/inst/extdata/thermo/opt.csv	2022-11-25 10:01:43 UTC (rev 755)
+++ pkg/CHNOSZ/inst/extdata/thermo/opt.csv	2022-11-27 11:43:35 UTC (rev 756)
@@ -1,2 +1,2 @@
-cutoff,E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Setchenow,Berman,maxcores,ionize.aa
-1E-10,J,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Bdot,bgamma0,NA,2,TRUE
+E.units,T.units,P.units,state,water,G.tol,Cp.tol,V.tol,varP,IAPWS.sat,paramin,ideal.H,ideal.e,nonideal,Setchenow,Berman,maxcores,ionize.aa
+J,C,bar,aq,SUPCRT92,100,1,1,FALSE,liquid,1000,TRUE,TRUE,Bdot,bgamma0,NA,2,TRUE

Modified: pkg/CHNOSZ/man/makeup.Rd
===================================================================
--- pkg/CHNOSZ/man/makeup.Rd	2022-11-25 10:01:43 UTC (rev 755)
+++ pkg/CHNOSZ/man/makeup.Rd	2022-11-27 11:43:35 UTC (rev 756)
@@ -47,34 +47,34 @@
 
 \examples{
 \dontshow{reset()}
-# the composition of a simple compound
+# Elemental composition of a simple compound
 makeup("CO2")     # 1 carbon, 2 oxygen
-# the formula of lawsonite, with a parenthetical part and a suffix
+# Formula of lawsonite, with a parenthetical part and a suffix
 makeup("CaAl2Si2O7(OH)2*H2O")
-# fractional coefficients are ok
+# Fractional coefficients are OK
 reddiv10 <- makeup("C10.6N1.6P0.1")
 10*reddiv10 # 106, 16, 1 (Redfield ratio)
 
-# the coefficient for charge is a number with a *preceding* sign
+# The coefficient for charge is a number with a *preceding* sign
 # e.g., ferric iron, with a charge of +3 is expressed as
 makeup("Fe+3")
-# transcribing the formula the way it appears in many 
+# Transcribing the formula the way it appears in many 
 # publications produces a likely unintended result:
 # 3 iron atoms and a charge of +1
 makeup("Fe3+")
 
-# these all represent a single negative charge, i.e., electron
+# These all represent a single negative charge, i.e., electron
 makeup("-1")
 makeup("Z-1+0")
 makeup("Z0-1")   # the "old" formula for the electron in thermo()$OBIGT
 makeup("(Z-1)")  # the current formula in thermo()$OBIGT
 
-# hypothetical compounds with negative numbers of elements
+# Hypothetical compounds with negative numbers of elements
 makeup("C-4(O-2)")   # -4 carbon, -2 oxygen
 makeup("C-4O-2")     # -4 carbon,  1 oxygen, -2 charge
 makeup("C-4O-2-2")   # -4 carbon, -2 oxygen, -2 charge
 
-# the 'sum' argument can be used to check mass and charge
+# The 'sum' argument can be used to check mass and charge
 # balance in a chemical reaction
 formula <- c("H2O", "H+", "(Z-1)", "O2")
 mf <- makeup(formula, c(-1, 2, 2, 0.5), sum = TRUE)

Modified: pkg/CHNOSZ/man/subcrt.Rd
===================================================================
--- pkg/CHNOSZ/man/subcrt.Rd	2022-11-25 10:01:43 UTC (rev 755)
+++ pkg/CHNOSZ/man/subcrt.Rd	2022-11-27 11:43:35 UTC (rev 756)
@@ -62,9 +62,9 @@
 
 A chemical reaction is defined if \code{coeff} is given.
 In this mode the standard molal properties of species are summed according to the stoichiometric \code{coeff}icients, where negative values denote reactants.
-Reactions that do not conserve elements are permitted; \code{subcrt} prints the missing composition needed to balance the reaction and produces a warning but computes anyway.
+An unbalanced reaction is signalled if the amount of any element on the reactant and product sides differs by more than 1e-7; in this case, \code{subcrt} prints the missing composition needed to balance the reaction and produces a warning but computes a result anyway.
 Alternatively, if \code{autobalance} is \code{TRUE}, the \code{\link{basis}} species of a system were previously defined, and all elements in the reaction are represented by the basis species, an unbalanced reaction given in the arguments to \code{subcrt} will be balanced automatically.
-The auto balancing doesn't change the reaction coefficients of any species that are do not correspond to basis species.
+The auto balancing doesn't change the reaction coefficients of any species in the reaction that are not among the basis species.
 
 If \code{logact} is provided, the chemical affinities of reactions are calculated.
 \code{logact} indicates the logarithms of activities (fugacities for gases) of species in the reaction; if there are fewer values of \code{logact} than number of species those values are repeated as necessary.
@@ -110,7 +110,7 @@
 }
 
 \value{
-For \code{subcrt}, a list of length two or three.
+A list of length two or three.
 If the properties of a reaction were calculated, the first element of the list (named \samp{reaction}) contains a dataframe with the reaction parameters; the second element, named \samp{out}, is a dataframe containing the calculated properties.
 Otherwise, the properties of species (not reactions) are returned: the first element, named \samp{species}, contains a dataframe with the species identification; the second element, named \samp{out}, is itself a list, each element of which is a dataframe of properties for a given species.
 If minerals with phase transitions are present, a third element (a dataframe) in the list indicates for all such minerals the stable phase at each grid point.

Modified: pkg/CHNOSZ/man/thermo.Rd
===================================================================
--- pkg/CHNOSZ/man/thermo.Rd	2022-11-25 10:01:43 UTC (rev 755)
+++ pkg/CHNOSZ/man/thermo.Rd	2022-11-27 11:43:35 UTC (rev 756)
@@ -45,7 +45,6 @@
     Note that the units of \code{G.tol} and \code{Cp.tol} depend on the \code{E_units} for each species in \code{thermo()$OBIGT}.
     Therefore, species with \code{E_units} of \samp{J} have a lower absolute tolerance for producing messages (because 4.184 J = 1 cal).
     \tabular{lll}{
-      \code{cutoff} \tab numeric \tab Cutoff below which values are taken to be zero [1e-10] (see \code{\link{makeup}})\cr
       \code{E.units} \tab character \tab The user's units of energy ([\samp{J}] or \samp{cal}) (see \code{\link{subcrt}})\cr
       \code{T.units} \tab character \tab The user's units of temperature ([\samp{C}] or \samp{K})\cr
       \code{P.units} \tab character \tab The user's units of pressure ([\samp{bar}] or \samp{MPa})\cr

