Added info to README

Analysis/.gitignore

@@ -0,0 +1 @@
+*.txt

Model/MRM0D/RunModel_BATS_MRM0D.sh

@@ -4,6 +4,8 @@
 
 #qfrac is the fraction of the surface area of the spherical particle covered by a single layer of bacteria, values greater than 1 mean that there is a second layer of bacteria
 
+#For higher resolution of max_epsilon, copy and paste this list into the code: 0.0000 0.0005 0.0010 0.0015 0.0020 0.0025 0.0030 0.0035 0.0040 0.0045 0.0050 0.0055 0.0060 0.0065 0.0070 0.0075 0.0080 0.0085 0.0090 0.0095 0.0100 0.0105 0.0110 0.0115 0.0120 0.0125 0.0130 0.0135 0.0140 0.0145 0.0150 0.0155 0.0160 0.0165 0.0170 0.0175 0.0180 0.0185 0.0190 0.0195 0.0200 0.0205 0.0210 0.0215 0.0220 0.0225 0.0230 0.0235 0.0240 0.0245 0.0250 0.0255 0.0260 0.0265 0.0270 0.0275 0.0280 0.0285 0.0290 0.0295 0.0300 0.0305 0.0310 0.0315 0.0320 0.0325 0.0330 0.0335 0.0340 0.0345 0.0350 0.0355 0.0360 0.0365 0.0370 0.0375 0.0380 0.0385 0.0390 0.0395 0.0400 0.0405 0.0410 0.0415 0.0420 0.0425 0.0430 0.0435 0.0440 0.0445 0.0450 0.0455 0.0460 0.0465 0.0470 0.0475 0.0480 0.0485 0.0490 0.0495 0.0500
+
 for max_epsilon in 0.0000 0.0100 0.0200 0.0300 0.0400 0.0500
 do
 for qfrac in 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 0.15 0.16 0.17 0.18 0.19 0.20 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 0.30 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40 0.41 0.42 0.43 0.44 0.45 0.46 0.47 0.48 0.49 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 0.60 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 0.75 0.76 0.77 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 0.90 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10

RCode/MRM0D_OptimalEpsilon.R

@@ -0,0 +1,93 @@
+#Change working directory to MicrobeReminModel_v1.0/RCode using the setwd() command or using the Misc menu.  
+#getwd() #shows the current working directory for the R gui.
+
+filepath = paste("../Output/MRM0D/", sep="")
+
+#Bacterial growth is assessed after 3 hours of intial spin-up.  Bacterial production is calculated over a 9 minute time interval which is the residence of exoenzyme in the particle.  The time step is 30 seconds. 
+tsegs1<-362  #Begin time for bacterial production calculation
+tsegs2<-379  #End time for bacterial production calculation
+
+#--------------------------
+#  Find Epsilon Optimum
+#--------------------------
+folderstate<-paste(filepath, "StateVariables/", sep="")
+statenames<-list.files(folderstate)
+
+folderbrates<-paste(filepath, "BacteriaRates/", sep="")
+bratesnames<-list.files(folderbrates)
+
+foldermrates<-paste(filepath, "MassTransferRates/", sep="")
+mratesnames<-list.files(foldermrates)
+
+analysis<-as.data.frame(matrix(NA, length(statenames), 6))
+colnames(analysis)<-c("maxe", "qfrac.init", "ba.init", "ba.prod", "enz.prod", "h.prod")
+
+for(a in 1:length(statenames)){
+
+state<-read.table(paste(folderstate, statenames[a], sep=""))
+colnames(state)<-c("time", "pom", "enz", "h", "ba", "hdom", "bf", "edom", "denz", "dedom")
+
+brates<-read.table(paste(folderbrates, bratesnames[a], sep=""))
+colnames(brates)<-c("time", "attach", "detach", "ba_grow", "bf_grow", "up_ba", "up_bf", "epsilon")
+
+mrates<-read.table(paste(foldermrates, mratesnames[a], sep=""))
+colnames(mrates)<-c("time", "pnum", "pom_dgd", "h_hdom", "ehl_k", "enz_dom", "denz_dom")
+
+analysis$maxe[a]<-as.numeric(substr(statenames[a], 20, 25))
+analysis$qfrac.init[a]<-as.numeric(substr(statenames[a], 32, 35))
+analysis$ba.init[a]<-state$ba[1]
+cperb<-5E-12  #carbon per bacteria
+analysis$ba.init[a]<-analysis$ba.init[a]/cperb/mrates$pnum[2] #number of bacteria per particle
+
+state<-state[tsegs1:tsegs2,]
+brates<-brates[tsegs1:tsegs2,]
+mrates<-mrates[tsegs1:tsegs2,]
+analysis$ba.prod[a]<-sum(state$ba*brates$ba_grow)
+analysis$enz.prod[a]<-sum(state$ba*brates$epsilon)
+analysis$h.prod[a]<-sum(state$enz*mrates$pom_dgd)
+
+}
+
+analysis$qfrac.init<-analysis$qfrac.init*100
+
+opt<-aggregate(analysis$ba.prod, list(analysis$qfrac.init), max)
+colnames(opt)<-c("qfrac.init", "ba.prod")
+opt<-merge(opt, analysis)
+colnames(opt)<-gsub("maxe", "opte", colnames(opt))
+opt<-opt[order(opt$qfrac.init),]
+
+opt<-opt[c("ba.init", "qfrac.init", "opte")]
+
+outfile<-paste("../Analysis/OptimalEpsilon.txt", sep="")
+write.table(opt, outfile, quote=FALSE, col.names=TRUE, row.names=FALSE, sep="\t")
+
+
+#---------------------------
+#   Plot Optimal Epsilon
+#---------------------------
+
+OutGraph<-paste("../Graphs/MRM0D1_OptimalEpsilon.ps", sep="")
+postscript(OutGraph, family="Helvetica", width=4, height=3.25)
+
+#quartz(width=4, height=3.25)
+par(oma=c(3,3,1,1))
+par(mar=c(1.5,1,1,0.5)+0.1)
+par(mfrow=c(1,1))
+par(xaxs="i")
+par(yaxs="i")
+par(cex.axis=1)
+par(cex.lab=1)
+par(cex.main=1)
+
+
+plot(opt$ba.init, opt$opte, type="l", ylim=c(0,0.05), xaxt="n", yaxt="n", lwd=2)
+axis(side=1, labels=TRUE)
+axis(side=2, labels=TRUE, las=1)
+
+
+mtext("Initial bacterial abundance per particle", side=1, cex=1, line=0.7 , adj=0.5, outer=TRUE)
+mtext(expression(paste("Optimal  ", epsilon)), side=2, cex=1, line=1.6 , adj=0.5, outer=TRUE)
+
+
+dev.off()
+

RCode/RunTest_BATS_MRM0D_OptimalEpsilon.sh

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+#!/bin/sh
+
+echo “——————————————————————————————”
+
+echo “MRM0D Optimal Epsilon”
+
+diff ../Analysis/OptimalEpsilon.txt ../TestFiles/MRM0D/OptimalEpsilon/OptimalEpsilon.txt
+if [ $? -eq 0 ]
+  then
+    echo “** PASSES TEST: Output Files Are The Same **”
+  else
+    echo “** FAILS TEST: Output Files Are Different **”
+fi
+
+echo “——————————————————————————————”