Bumping to 0.3.6. Modified RepSol and AddProp

DESCRIPTION

 Package: RedModRphree
 Title: Utilities Leveraging the R Interface to the PHREEQC Geochemical Solver 
-Version: 0.3.4
+Version: 0.3.6
 Authors@R: c(person(given = "Marco",
                     family = "De Lucia",
                     email = "delucia@gfz-potsdam.de",

R/Rphree_Utils.R

 ### Utility functions for RedModRphree
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
-### Time-stamp: "Last modified 2021-05-06 16:05:40 delucia"
+### Time-stamp: "Last modified 2021-06-26 17:40:57 delucia"
 
 ##' Replicates an input buffer containing only one SOLUTION, taking
-##' care of SOLUTION/KINETICS/PURE identifiers. Eventually insert a
-##' block (e.g: PUNCH) just once under the first SOLUTION.
+##' care of SOLUTION/KINETICS/PURE identifiers. Eventually inserts a
+##' block (e.g: PUNCH, or PHASES) just once under the first SOLUTION.
 ##'
 ##' Analogous to standard \code{rep} function.
 ##' @title Replicate a SOLUTION 
@@ -81,9 +81,12 @@ AddProp <- function(input, name, values, cat, kinpar=NULL, first=NULL)
     val <- as.character(values)
     nval <- length(val)
     nsim <- length(marksol <- grep("^SOLUTION",input))
+    nends <- length(marksend <- grep("^END",input))
 
     if (nval != nsim && nsim != 1)
         stopmsg("Lengths of simulation and values to add do not agree!")
+    if (nends != nsim)
+        stopmsg("Please explicitely add END at the bottom of your input script!")
 
     if (cat == "tot") {
         if (nsim == 1) {
@@ -107,8 +110,33 @@ AddProp <- function(input, name, values, cat, kinpar=NULL, first=NULL)
     }
 
     if (cat == "pphases") {
-        markpure <- grep("PURE", input)
-        if (nsim == 1) {
+        markpure <- grep("^PURE|^EQUILIBRIUM", input)
+        ## check if a line containing "PURE" or "EQUILIBRIUM_PHASE" is
+        ## actually there, if not add it just before "END"
+        addKeyword <- ifelse(length(markpure)==0, TRUE, FALSE)
+        ## create "space" in the solution vector and add keyword
+        ## "PURE" if needed
+        if (addKeyword) {
+            ## msg ("addKeyword TRUE")
+            if (nsim==1) {
+                markpure <- length(input)-1 ## the lines before "END"
+                ## msg("markpure", markpure)
+                tmp <- c(input[1:markpure], "PURE 1",input[seq(markpure+1,length(input))])
+                ## msg(tmp)
+            } else {
+                markpure <- marksend-1
+                tmp <- character(length(input) + nsim)
+                tmp[markpure] <- paste("PURE", seq_along(nsim))
+                rest <- seq_along(tmp)[-markpure]
+                tmp[rest] <- input
+            }
+        }
+        ## now we are ensured that proper keywords are present
+        input <- tmp
+        ## update markpure
+        markpure <- grep("^PURE", input)
+        
+        if (nsim == 1) { ## we don't need to "RepSol"
             tmp <- c(input[1:markpure], paste(name, val[1]), input[(markpure + 1):length(input)])
             if (nval != 1) 
                 newinp <- Distribute(tmp, reg, val, first)
@@ -122,7 +150,7 @@ AddProp <- function(input, name, values, cat, kinpar=NULL, first=NULL)
             newinp <- Distribute(tmp, reg, values, first)
         }
     }    
-
+    
     if (cat == "kin") {
         if (nsim != 1)
             stopmsg(" with KINETICS is able to handle only one simul at a time!")

man/RepSol.Rd

@@ -19,8 +19,8 @@ A buffer upon which RunPQC can be called
 }
 \description{
 Replicates an input buffer containing only one SOLUTION, taking
-care of SOLUTION/KINETICS/PURE identifiers. Eventually insert a
-block (e.g: PUNCH) just once under the first SOLUTION.
+care of SOLUTION/KINETICS/PURE identifiers. Eventually inserts a
+block (e.g: PUNCH, or PHASES) just once under the first SOLUTION.
 }
 \details{
 Analogous to standard \code{rep} function.