diff --git a/.Rhistory b/.Rhistory
index b2bcc67..5bee821 100644
--- a/.Rhistory
+++ b/.Rhistory
@@ -1 +1,5 @@
 install.packages("RBBGCMuso_0.1.8.tar.gz")
+install.packages("RBBGCMuso_0.1.8.tar.gz")
+install.packages("RBBGCMuso_0.1.8.tar.gz")
+install.packages("RBBGCMuso_0.1.8.tar.gz")
+install.packages("RBBGCMuso_0.1.8.tar.gz")
diff --git a/RBBGCMuso/DESCRIPTION b/RBBGCMuso/DESCRIPTION
index 0bae58d..65da841 100644
--- a/RBBGCMuso/DESCRIPTION
+++ b/RBBGCMuso/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RBBGCMuso
 Title: What the Package Does (one line, title case)
-Version: 0.1.8
+Version: 0.1.9.0-1
 Authors@R: person("Roland", "Hollos", , "hollorol@gmail.com", role = c("aut", "cre"))
 Description: What the package does (one paragraph)
 License: GPL-2
diff --git a/RBBGCMuso/R/calibMuso.R b/RBBGCMuso/R/calibMuso.R
index 99d588d..c490c6d 100644
--- a/RBBGCMuso/R/calibMuso.R
+++ b/RBBGCMuso/R/calibMuso.R
@@ -14,6 +14,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
 
     ##Copy the variables from settings
     inputloc <- settings$inputloc
+    outputloc <- settings$outputloc
     executable <- settings$executable
     ininput <- settings$ininput
     epc <- settings$epcinput
@@ -32,7 +33,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     }
     
     if(aggressive==TRUE){
-        cleanupMuso()
+        cleanupMuso(location=outputloc)
     }
     
     ##change the epc file if and only if there are given parameters
@@ -64,12 +65,12 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
 
     
     
-    logspinup<-list.files(inputloc)[grep("log$",list.files(inputloc))]#load the logfiles
+    logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
     if(length(logspinup)==0){
         return("Modell Failure")#in that case the modell did not create even a logfile
     }
     
-    spincrash<-tail(readLines(paste(inputloc,logspinup,sep=""),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
+    spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
     
     if(!spincrash){##If spinup did not crashed, run the normal run.
         
@@ -102,13 +103,13 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     }
 
     
-    logfiles <- list.files(inputloc)[grep("log$",list.files(inputloc))]#creating a vector for logfilenames
+    logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
 
 ###############################################    
 #############LOG SECTION#######################
 ###############################################
     
-    perror<-as.numeric(as.vector(lapply(paste(inputloc,logfiles,sep=""),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
+    perror<-as.numeric(as.vector(lapply(paste(outputloc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
     
     if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
         #If log or ERROR directory does not exists create it!
@@ -186,7 +187,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
                  
              }}
     
-    cleanupMuso()
+    cleanupMuso(location=outputloc)
     if(errorsign==1){
         return("Modell Failure")
     }
diff --git a/RBBGCMuso/R/cleanup.R b/RBBGCMuso/R/cleanup.R
index d8d87f5..bb0c223 100644
--- a/RBBGCMuso/R/cleanup.R
+++ b/RBBGCMuso/R/cleanup.R
@@ -1,4 +1,4 @@
-cleanupMuso <- function(location=NULL,deep=FALSE){
+cleanupMuso <- function(location=NULL, simplicity=TRUE,deep=FALSE){
 
     whereAmI <- getwd()
     if(!is.null(location)){
@@ -44,11 +44,13 @@ cleanupMuso <- function(location=NULL,deep=FALSE){
         )
         
     }
-    
-    file.remove(
-        grep("(out$)|(endpoint$)|(log$)",
-             list.files(), value = T)
-    )
+    if(!simplicity){    
+        file.remove(
+            grep("(out$)|(endpoint$)|(log$)",
+                 list.files(), value = T)
+        )} else {
+             file.remove(grep("log$",list.files(),value = T))
+         }
 
     setwd(whereAmI)
     
diff --git a/RBBGCMuso/R/getOutput.R b/RBBGCMuso/R/getOutput.R
index 598de78..92d4763 100644
--- a/RBBGCMuso/R/getOutput.R
+++ b/RBBGCMuso/R/getOutput.R
@@ -12,7 +12,7 @@ getthespecdata<-function(settings,colnumbers){
 }
 
 getdailyout<-function(settings){
-  binaryname<-paste(settings$inputloc,settings$outputname,".dayout",sep="")
+  binaryname<-paste(settings$inputloc,settings$outputnames,".dayout",sep="")
   d<-file(binaryname,"rb")
   dayoutput<-matrix(readBin(d,"double",size=4,n=(settings$numdata[1])),(settings$numyears*365),byrow=TRUE)
   close(d)
diff --git a/RBBGCMuso/R/rungetMuso.R b/RBBGCMuso/R/rungetMuso.R
index 9652215..4fb3bca 100644
--- a/RBBGCMuso/R/rungetMuso.R
+++ b/RBBGCMuso/R/rungetMuso.R
@@ -14,6 +14,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
 
     ##Copy the variables from settings
     inputloc <- settings$inputloc
+    outputloc <- settings$outputloc
     executable <- settings$executable
     ininput <- settings$ininput
     epc <- settings$epcinput
@@ -32,7 +33,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     }
     
     if(aggressive==TRUE){
-        cleanupMuso()
+        cleanupMuso(location=outputloc)
     }
 
     ##We change the working directory becase of the model, but we want to avoid sideeffects, so we save the current location and after that we will change everything to it.
@@ -59,12 +60,12 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
 
     
     
-    logspinup<-list.files(inputloc)[grep("log$",list.files(inputloc))]#load the logfiles
+    logspinup<-list.files(outputloc)[grep("log$",list.files(outputloc))]#load the logfiles
     if(length(logspinup)==0){
         return("Modell Failure")#in that case the modell did not create even a logfile
     }
     
-    spincrash<-tail(readLines(paste(inputloc,logspinup,sep=""),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
+    spincrash<-tail(readLines(paste(outputloc,logspinup,sep="/"),-1),1)==0 #If the last line in the logfile is 0 There are mistakes so the spinup crashes
     
     if(!spincrash){##If spinup did not crashed, run the normal run.
         
@@ -97,13 +98,13 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
     }
 
     
-    logfiles <- list.files(inputloc)[grep("log$",list.files(inputloc))]#creating a vector for logfilenames
+    logfiles <- list.files(outputloc)[grep("log$",list.files(outputloc))]#creating a vector for logfilenames
 
 ###############################################    
 #############LOG SECTION#######################
 ###############################################
     
-    perror<-as.numeric(as.vector(lapply(paste(inputloc,logfiles,sep=""),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
+    perror<-as.numeric(as.vector(lapply(paste(outputloc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1)))) #vector of spinup and normalrun error
     
     if((debugging=="stamplog")|(debugging==TRUE)){#If debugging option turned on
         #If log or ERROR directory does not exists create it!
@@ -181,7 +182,7 @@ rungetMuso <- function(settings, timee="d", debugging=FALSE, logfilename=NULL, k
                  
              }}
     
-    cleanupMuso()
+    cleanupMuso(location=outputloc)
     if(errorsign==1){
         return("Modell Failure")
     }
diff --git a/RBBGCMuso/R/setupMuso.R b/RBBGCMuso/R/setupMuso.R
index 97aff0e..daa59fd 100644
--- a/RBBGCMuso/R/setupMuso.R
+++ b/RBBGCMuso/R/setupMuso.R
@@ -26,8 +26,7 @@ setupMuso <- function(executable=NULL,
 
     if(is.null(inputloc)){
         inputloc<- "./"
-    }
-    
+    } else {
     inp <- unlist(strsplit(inputloc,"")) #This is the charactervector of the given imput location
 
     if(inp[length(inp)]!="/"){
@@ -37,10 +36,8 @@ setupMuso <- function(executable=NULL,
     }# If inp not ends in / paste one at the end, then make a string, that will be the new inputloc
 
     ##Example: "a/b/c ==> a/b/c/"
-    
-    if(is.null(outputloc)){
-        outputloc<-inputloc
     }
+    inichangedp <- FALSE
 
     if(is.null(ininput)){
         spinups<-grep("s.ini$",list.files(inputloc),value=TRUE)
@@ -60,7 +57,9 @@ setupMuso <- function(executable=NULL,
     ##read the ini files for the further changes
 
     inifiles<-lapply(ininput, function (x) readLines(x,-1))
-
+    inifiles[[1]] <- gsub("\\","/", inifiles[[1]],fixed=TRUE) #replacing \ to /
+    inifiles[[2]] <- gsub("\\","/", inifiles[[2]],fixed=TRUE) #replacing \ to /
+    
     if(is.null(epcinput)){
         epcflag=TRUE
         epcinput[1] <-  unlist(strsplit(grep(" EPC file name",inifiles[[1]],value=TRUE),"[\ \t]"))[1]
@@ -230,6 +229,15 @@ setupMuso <- function(executable=NULL,
         
 }
 ##    outputname<-unlist(read.table(ininput[2],skip=93,nrows = 1))[1]
+
+
+    if(is.null(outputloc)){
+    ##  outputloc<-paste((rev(rev(unlist(strsplit(outputname,"/")))[-1])),collapse="/")
+        outputloc <- dirname(outputname)
+    }
+
+    
+    
     inputfiles<-c(ininput,epcinput,metinput)
     numdata<-rep(NA,3)
     numyears <-  as.numeric(unlist(strsplit(grep("simulation years",inifiles[[2]],value=TRUE),"[\ \t]"))[1])
@@ -241,6 +249,11 @@ setupMuso <- function(executable=NULL,
     numdata[2]<-numyears*numvalues*12
     numdata[3]<-numyears*numvalues
 
+    ##Writing out changed ini-file
+
+    writeLines(inifiles[[1]],ininput[1])
+    writeLines(inifiles[[2]],ininput[2])
+    
     settings = list(executable = executable,
                     calibrationpar = calibrationpar,
                     outputloc=outputloc,
diff --git a/RBBGCMuso_0.1.8.tar.gz b/RBBGCMuso_0.1.8.tar.gz
index c7d248a..278d91f 100644
Binary files a/RBBGCMuso_0.1.8.tar.gz and b/RBBGCMuso_0.1.8.tar.gz differ
diff --git a/RBBGCMuso_0.1.9.0-1.tar.gz b/RBBGCMuso_0.1.9.0-1.tar.gz
new file mode 100644
index 0000000..7e4fdbc
Binary files /dev/null and b/RBBGCMuso_0.1.9.0-1.tar.gz differ