diff --git a/DESCRIPTION b/DESCRIPTION
index 8aa3d04df8814028f52a59a1cb4cc90d87fdbac7..aaddf6e367f2e97bc0b634ec3f50f744e8ed0b2d 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: hydroPSO
Type: Package
Title: Model-Independent Particle Swarm Optimisation for Environmental Models
Version: 0.1-56
-Date: 2012-06-12
+Date: 2012-06-13
Author: Mauricio Zambrano-Bigiarini [aut, cre] and Rodrigo Rojas [ctb]
Author@R: c(person("Mauricio", "Zambrano-Bigiarini", email = "mzb.devel@gmail.com", role=c("aut", "cre") ), person("Rodrigo", "Rojas", email = "Rodrigo.RojasMujica@gmail.com", role=c("ctb") ) )
Maintainer: Mauricio Zambrano-Bigiarini <mzb.devel@gmail.com>
diff --git a/NEWS b/NEWS
index b1b9da413ffa009e0feaca51024d0f61d1b1bde1..1f70c0c6f718cb9b5bf9ee5bc75c73218d7b6dc5 100755
--- a/NEWS
+++ b/NEWS
@@ -2,10 +2,10 @@ NEWS/ChangeLog for hydroPSO
--------------------------
-0.1-56 12-Jun-2012
+0.1-56 13-Jun-2012
o 'hydroPSO' : -) much less memory consumption for large values of 'maxit' and/or 'npart'.
- The files 'BestParamPerIter.txt', 'PbestPerIter.txt', and 'LocalBestPerIter.txt' are now written at the end of
- each iteration, and not at the end of the main algorithm
+ The files 'BestParamPerIter.txt', 'PbestPerIter.txt', 'LocalBestPerIter.txt', 'Velocities.txt' are now written at the end of
+ each iteration, and not at the end of the main algorithm (so the corresponding local variables were removed)
-) the convergence of the algorithm controlled by 'reltol' is now defined by : reltol <= normalised swarm radius,
instead of reltol <= [ gbest(iter) / ( gbest(iter-1) +reltol ) ]
-) 'PbestPerIter.txt' output file: now it has an additional first column labelled "Iter", with the iteration number
diff --git a/R/PSO_v2012.R b/R/PSO_v2012.R
index 272e697d8b937d65f672b09b0fa4a47fcaec83a7..f11c143afcf3453fa896e51453eea0b73d59edca 100755
--- a/R/PSO_v2012.R
+++ b/R/PSO_v2012.R
@@ -1104,7 +1104,7 @@ Random.Topology.Generation <- function(npart, K,
# Updates: Dec-2010 #
# May-2011 ; 28-Oct-2011 ; 14-Nov-2011 ; 23-Nov-2011 ; #
# 15-Jan-2012 ; 23-Jan-2012 ; 30-Jan-2012 ; 23-Feb-2012 ; 23-Mar-2012 #
-# 12-Jun-2012 #
+# 13-Jun-2012 #
################################################################################
# 'lower' : minimum possible value for each parameter
# 'upper' : maximum possible value for each parameter
@@ -1725,14 +1725,11 @@ hydroPSO <- function(
Xt.fitness <- matrix(rep(fn.worst.value, maxit*npart), ncol=npart, nrow=maxit, byrow=TRUE)
colnames(Xt.fitness) <- paste("Part", 1:npart, sep="")
- rownames(Xt.fitness) <- paste("iter.", 1:maxit, sep="")
-
- velocities <- matrix(rep(NA, (n+2)*maxit*npart), ncol=(n+2), nrow=maxit*npart, byrow=TRUE)
- colnames(velocities) <- c("Iter", "Part", param.IDs)
+ rownames(Xt.fitness) <- paste("iter.", 1:maxit, sep="")
if (topology != "random") {
nc <- K
- ifelse(trunc(K/2) != ceiling(K/2), N <- (K-1)/2, N <- K/2)
+ ifelse(trunc(K/2) != ceiling(K/2), N <- (K-1)/2, N <- K/2)
ifelse(trunc(K/2) != ceiling(K/2), NN <- 1, NN <- 0)
X.neighbours <- matrix(rep(-NA, nc*npart), ncol=nc, nrow=npart, byrow=TRUE)
@@ -2063,10 +2060,6 @@ hydroPSO <- function(
Xt.fitness[iter, 1:npart] <- apply(X, fn, MARGIN=1)
GoF <- Xt.fitness[iter, 1:npart]
- velocities[(npart*(iter-1)+1):(npart*iter), 1] <- iter
- velocities[(npart*(iter-1)+1):(npart*iter), 2] <- 1:npart
- velocities[(npart*(iter-1)+1):(npart*iter), 3:(2+n)] <- V
-
nfn <- nfn + npart
if (write2disk) {
@@ -2101,10 +2094,6 @@ hydroPSO <- function(
GoF <- as.numeric(hydromod.out[["GoF"]])
Xt.fitness[iter, part] <- GoF
- velocities[npart*(iter-1)+part, 1] <- iter
- velocities[npart*(iter-1)+part, 2] <- part
- velocities[npart*(iter-1)+part, 3:(2+n)] <- V[part,]
-
if(is.finite(GoF)) nfn <- nfn + 1
if (write2disk) {
@@ -2133,33 +2122,6 @@ hydroPSO <- function(
} # ELSE end
-
- if (write2disk) {
- for ( part in (1:npart) ) {
- # File 'Particles.txt' #
- if(is.finite(Xt.fitness[iter, part])) {
- writeLines(as.character( c(iter, part,
- formatC(Xt.fitness[iter, part], format="E", digits=digits, flag=" "), #GoF
- formatC(X[part, ], format="E", digits=digits, flag=" ")
- ) ), Particles.TextFile, sep=" ")
- } else writeLines(as.character( c(iter, part, "NA",
- formatC(X[part, ], format="E", digits=digits, flag=" ")
- ) ), Particles.TextFile, sep=" ")
- writeLines("", Particles.TextFile)
-
- # File 'Velocities.txt' #
- if(is.finite(Xt.fitness[iter, part])) {
- writeLines( as.character( c(iter, part,
- formatC(Xt.fitness[iter, part], format="E", digits=digits, flag=" "), # GoF
- formatC(V[part, ], format="E", digits=digits, flag=" ")
- ) ), Velocities.TextFile, sep=" ")
- } else writeLines( as.character( c(iter, part, "NA",
- formatC(V[part, ], format="E", digits=digits, flag=" ")
- ) ), Velocities.TextFile, sep=" ")
- writeLines("", Velocities.TextFile)
- } # FOR end
- } # IF end
-
if ( plot ) {
ifelse(MinMax == "max", lgof <- max(GoF, na.rm=TRUE), lgof <- min(GoF, na.rm=TRUE))
colorRamp= colorRampPalette(c("darkred", "red", "orange", "yellow", "green", "darkgreen", "cyan"))
@@ -2246,6 +2208,33 @@ hydroPSO <- function(
################### Particles Loop (j) - Start ########################
##########################################################################
for (j in 1:npart) {
+
+ if (write2disk) {
+
+ # File 'Particles.txt' #
+ if(is.finite(Xt.fitness[iter, part])) {
+ writeLines(as.character( c(iter, j,
+ formatC(Xt.fitness[iter, j], format="E", digits=digits, flag=" "), #GoF
+ formatC(X[j, ], format="E", digits=digits, flag=" ")
+ ) ), Particles.TextFile, sep=" ")
+ } else writeLines(as.character( c(iter, j, "NA",
+ formatC(X[j, ], format="E", digits=digits, flag=" ")
+ ) ), Particles.TextFile, sep=" ")
+ writeLines("", Particles.TextFile)
+
+ # File 'Velocities.txt' #
+ if(is.finite(Xt.fitness[iter, j])) {
+ writeLines( as.character( c(iter, j,
+ formatC(Xt.fitness[iter, j], format="E", digits=digits, flag=" "), # GoF
+ formatC(V[j, ], format="E", digits=digits, flag=" ")
+ ) ), Velocities.TextFile, sep=" ")
+ } else writeLines( as.character( c(iter, j, "NA",
+ formatC(V[j, ], format="E", digits=digits, flag=" ")
+ ) ), Velocities.TextFile, sep=" ")
+ writeLines("", Velocities.TextFile)
+
+ } # IF end
+
if ( best.update == "async" ) {
tmp <- async.update.pgbests(x=X[j,],