Fixed demos with imports, out_bal & co in ReactTrans now assigned at the end to GlobalEnv

R/Rphree_Kinetics.R

 ##  Functions for dealing with simulations with kinetics
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
-### Time-stamp: "Last modified 2021-04-28 16:06:07 delucia"
+### Time-stamp: "Last modified 2021-04-28 17:23:36 delucia"
 
 ##' This function runs the generated input buffer (or a list thereof)
 ##' through \code{phreeqc}, which has been already loaded as
 ##' dependency. Also the database must be previously and explicitely
-##' loaded by the user using, e.g., \code{db <-
-##' RPhreeFile('/path/to/database.dat', is.db=TRUE)} followed by
-##' \code{phreeqc::phrLoadDatabaseString(db)} or using one of the
-##' databases included in \code{phreeqc}, e.g.,
-##' \code{phreeqc::phrLoadDatabaseString(phreeqc.dat)}.
-##'
-##' Parallelization is achieved using \code{%dopar%} from package
+##' loaded by the user using, e.g.,
+##' \code{db <- RPhreeFile('/path/to/database.dat', is.db=TRUE)}
+##' followed by
+##' \code{phreeqc::phrLoadDatabaseString(db)}
+##' or using one of the databases included in \code{phreeqc}, e.g.,
+##' \code{phreeqc::phrLoadDatabaseString(phreeqc.dat)}
+##' Parallelization is achieved using \code{\%dopar\%} from package
 ##' \code{foreach}, while the backend should have been previously set
 ##' with appropriate call to \code{doParallel}. At the moment the
 ##' function doesn't check that the SELCTED_OUTPUT block is
@@ -51,8 +51,6 @@ RunPQC <- function(input, procs=1, second=TRUE) {
         }
     } else {
         ## go parallel!
-
-        ## old one
         ## res <- parallel::mclapply(input, .runPQC, mc.silent=TRUE, mc.cores=procs)
         res <- foreach::foreach(i=seq_along(input), .combine=rbind) %dopar% .runPQC(input[[i]], onlysecond=second)
 

R/Rphree_Pourbaix.R

 ### Licence: LGPL version 2.1
-## Time-stamp: "Last modified 2021-04-28 17:04:27 delucia"
+## Time-stamp: "Last modified 2021-04-28 17:20:11 delucia"
 
 ##' @title Revert a string
 ##' @param x character vector. All element of the vector will be
@@ -439,7 +439,7 @@ Pourbaix <- function(element, pe=seq(-5,8), pH=seq(6,12), Tc=25, Patm=1, base, f
         if (missing(ann.title)) {
             mymain <- paste("Pourbaix diagram for",
                             ifelse(missing(element), "the specified system", ifelse(has_valence, valence, element)),
-                            "\n T=", Tc, "\U3f43 C  /  P=", Patm, "atm")
+                            "\n T=", Tc, "\u00B0C  /  P=", Patm, "atm")
         } else
             mymain <- ann.title
         

R/Rphree_ReactTrans.R

 ##  Functions for dealing with surrogate simulations
 
 ### Marco De Lucia, delucia@gfz-potsdam.de, 2009-2021
-### Time-stamp: "Last modified 2021-04-28 15:54:48 delucia"
+### Time-stamp: "Last modified 2021-04-28 18:13:39 delucia"
 
 
 ##' This function takes the current state of a chemical system in form
@@ -294,8 +294,6 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
     spr_string <- paste0("%0", pad,"d")
     names(saved_complete) <- paste0("step_",sprintf(spr_string,seq(0,maxiter)))
 
-    utils::globalVariables(c("out_inp","out_res","out_bal"))
-
     out_inp <- vector(mode="list",length=length(maxiter))
     out_res <- vector(mode="list",length=length(maxiter))
     out_bal <- vector(mode="list",length=length(maxiter))
@@ -406,7 +404,6 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
         # so that the first run on Rphree is actually one and the next ones end
         time <- time + dt
         iter <- iter + 1
-        #cat("ENTERING ADV","\n")
 
         ## transform the pH/pe back into activities
         state_T <- AdvectionPQC(pH2Act(state_C), inflow=bound, dx=dx, dt=dt, U=U)
@@ -491,6 +488,10 @@ ReactTranspBalanceEq <- function(setup, init, maxtime, step=c("time","iter","fix
         msg("Parallelization cluster stopped")
     }
 
+    msg("assign out_balance, out_input and out_results to global environment for possible later use")
+    assign("out_balance", out_bal, envir = .GlobalEnv)
+    assign("out_results", out_res, envir = .GlobalEnv)
+    assign("out_input",   out_inp, envir = .GlobalEnv)
 
     msg("total time of chemistry: ",round(sum(timing[,3]),3),"seconds")
     msg("total number of simulations: ",sum(timing[,1]))
@@ -604,8 +605,6 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
     spr_string <- paste0("%0", pad,"d")
     names(saved_complete) <- paste0("step_",sprintf(spr_string,seq(0,maxiter)))
 
-    utils::globalVariables(c("out_inp","out_res","out_bal"))
-    
     out_inp <- vector(mode="list",length=length(maxiter))
     out_res <- vector(mode="list",length=length(maxiter))
     out_bal <- vector(mode="list",length=length(maxiter))
@@ -711,7 +710,6 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
         # so that the first run on Rphree is actually one and the next ones end
         time <- time + dt
         iter <- iter + 1
-        #cat("ENTERING ADV","\n")
 
         ## transform the pH/pe back into activities
         state_T <- AdvectionPQC(pH2Act(state_C), inflow=bound, dx=dx, dt=dt, U=U)
@@ -737,10 +735,8 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
             out_bal[[iter]] <- bal
             totbal <- apply(bal, 1, mae)
             
-            ## cat(":: Surrogate Balance Summary:\n")
             ## print(summary(totbal))
             ## tol2 <- unname(quantile(totbal, .85))
-            ## cat(" :RT: Balance Checked\n")
             
             nonok <- which(totbal>tol)
             if (length(nonok)>0){
@@ -804,6 +800,11 @@ ReactTranspBalanceKin <- function(setup, init, maxtime, step=c("time","iter","fi
         msg("Parallelization cluster stopped")
     }
 
+    msg("assign out_balance, out_input and out_results to global environment for possible later use")
+    assign("out_balance", out_bal, envir = .GlobalEnv)
+    assign("out_results", out_res, envir = .GlobalEnv)
+    assign("out_input",   out_inp, envir = .GlobalEnv)
+
     msg("total time of chemistry: ",round(sum(timing[,3]),3),"seconds")
     msg("total number of simulations: ",sum(timing[,1]))
     msg(" Bye.")

demo/demo-eq-surr-RF.R

 ### Licence: LGPL version 2.1
-## Time-stamp: "Last modified 2018-08-29 15:15:50 delucia"
+## Time-stamp: "Last modified 2021-04-28 18:23:19 delucia"
+
+require(e1071)
+require(import)
 
 db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat", package="RedModRphree"), is.db=TRUE)
 phreeqc::phrLoadDatabaseString(db)

demo/demo-kin-surr-RF.R

 ## Licence: LGPL version 2.1
-## Time-stamp: "Last modified 2018-05-06 21:29:53 delucia"
+## Time-stamp: "Last modified 2021-04-28 18:27:32 delucia"
 
 
 library(RedModRphree)
+require(e1071)
+require(import)
+
 db <- RPhreeFile(system.file("extdata", "phreeqc_kin.dat", package="RedModRphree"), is.db=TRUE)
 
 base <- c("SOLUTION 1", "units mol/kgw", "temp 25.0", "water 1",

man/RunPQC.Rd

@@ -22,14 +22,17 @@ a data.frame containing the SELECTED_OUTPUT, ordered if
 This function runs the generated input buffer (or a list thereof)
 through \code{phreeqc}, which has been already loaded as
 dependency. Also the database must be previously and explicitely
-loaded by the user using, e.g., \code{db <-
-RPhreeFile('/path/to/database.dat', is.db=TRUE)} followed by
-\code{phreeqc::phrLoadDatabaseString(db)} or using one of the
-databases included in \code{phreeqc}, e.g.,
-\code{phreeqc::phrLoadDatabaseString(phreeqc.dat)}.
-}
-\details{
-
+loaded by the user using, e.g.,
+\code{db <- RPhreeFile('/path/to/database.dat', is.db=TRUE)}
+followed by
+\code{phreeqc::phrLoadDatabaseString(db)}
+or using one of the databases included in \code{phreeqc}, e.g.,
+\code{phreeqc::phrLoadDatabaseString(phreeqc.dat)}
+Parallelization is achieved using \code{\%dopar\%} from package
+\code{foreach}, while the backend should have been previously set
+with appropriate call to \code{doParallel}. At the moment the
+function doesn't check that the SELCTED_OUTPUT block is
+well-formed, so this is responsibility of the user.
 }
 \author{
 MDL