Completed the GcmcTutorial. Modified grompy.__init__ to accomodate for

non-standard locations of libc.s0.6.

Change-Id: Ib15844de40d89cd6b807e82673a8e983f5d9903b

GcmcTutorial/GcmcLj/DoBlockAveraging.sh

@@ -0,0 +1,42 @@
+#! /bin/bash
+
+MCReportFiles=`find -type f -name MCReport.prod.dat`
+
+echo "# mu [kJ/mol] Rho [1/(nm^3)] Err Rho [1/(nm^3)]" > rho_of_mu.dat
+for MCReportFile in $MCReportFiles
+do
+    grep -v \# $MCReportFile | awk '{print $1,$4}' > Rho.xvg
+    g_analyze -f Rho.xvg -ee Err.xvg > /dev/null 2>&1
+    rm -f \#*
+    Mu=`echo $MCReportFile | sed -e s/"\/"/\ /g | awk '{print $2}' | sed -e s/mu//`
+    AvRho=`grep \"av Err.xvg | sed -e s/\"//g | awk '{print $(NF)}'`
+    SdRho=`grep \"ee Err.xvg | sed -e s/\"//g | awk '{print $(NF)}'`
+    echo $Mu $AvRho $SdRho
+done | sort -n >> rho_of_mu.dat
+rm Rho.xvg Err.xvg
+
+NA="6.0221415e23"
+MCReportFile=`echo $MCReportFiles | awk '{print $(NF)}'`
+Lambda3=`grep "\# De Broglie Wavelength\^3 \[l\/mol\]" $MCReportFile | awk '{print $(NF-4)}'` #l/mol
+DmPerM=10.0
+NmPerM=1.0e9
+Kilo=1000.0
+R=8.314472 #J/mol/K
+T=`grep "\# De Broglie Wavelength\^3 \[l\/mol\]" $MCReportFile | awk '{print $(NF-1)}'` #K
+
+echo "#  mu [kJ/mol] Rho [mol/l] Err Rho [mol/l]"                                   > rho_of_mu_in_mol_p_l.dat
+grep -v \# rho_of_mu.dat | awk '{f='$NmPerM'^3/'$Kilo'/'$NA';print $1,f*$2,f*$3}'  >> rho_of_mu_in_mol_p_l.dat
+
+echo "# rho [mol/l] sdrho [mol/l] mu [kJ/mol] muid[kJ/mol] muex [kJ/mol] sdmuex [kJ/mol]" > mu_of_rho_in_mol_p_l.dat
+grep -v \# rho_of_mu_in_mol_p_l.dat | awk '
+{
+rho=$2;
+sdrho=$3;
+mu=$1;
+muid='$R'*'$T'*log(rho*'$Lambda3')/'$Kilo';
+muex=mu-muid;
+sdmuex='$R'*'$T'/rho*sdrho/'$Kilo';
+print rho, sdrho, mu, muid, muex, sdmuex;
+}' >> mu_of_rho_in_mol_p_l.dat
+
+exit

GcmcTutorial/GcmcLj/RunEos.sh

@@ -0,0 +1,29 @@
+#! /bin/bash
+
+GMXINSTALLDIR="../../gromacs/gromacs-4.0.7/gromacs-4.0.7-git/install/"
+source ../SourceGromPyEnv.sh
+
+InputParFile="start.dat"
+MuList=`grep -v \# $InputParFile | awk '{print $3}' | sort -n`
+TprDir=$PWD"/tpr"
+PyLogFile="py.log"
+NMin=0
+NMax=426
+GCMCMol="W"
+GcmcPy=testHybrid.py
+
+for i in $MuList
+do
+    Mu=$i
+    NStart=`grep "mu"$i $InputParFile| awk '{print $2}'`
+    echo "Performing MuVT simulation @ Mu=$Mu ..."
+    cd "mu$i"
+        time ../../../$GcmcPy $TprDir $Mu $NStart $GCMCMol $NMin $NMax 2> /dev/null > $PyLogFile
+        rm -f \#*
+        gzip -f md.log
+        gzip -f py.log
+        echo
+    cd ../
+done
+
+exit

GcmcTutorial/GcmcLj/gro/GenerateStartingStructures.sh

@@ -0,0 +1,44 @@
+#! /bin/bash
+
+EXPECTED_N_ARGS=3
+if [ $# -ne $EXPECTED_N_ARGS ]; then
+   echo "Input the correct amount of arguments!"
+   echo "Usage:"
+   echo "------"
+   echo "./GenerateStartingStructures.sh \"StartOfNRange\" \"EndOfNRange\" \"WInputN.gro\""
+   echo "Example: ./GenerateStartingStructures.sh 1 430 W400.gro"
+   echo "EXITING..."
+   exit 1
+fi
+
+NStart=$1
+NEnd=$2
+NInputFile=$3
+NInput=`echo $NInputFile | cut -d. -f1 | sed -e s/W//`
+
+declare -i N=$NStart
+while [ $N -lt $NInput ]
+do
+    head -1 $NInputFile                     > tmp.gro
+    echo $N                                >> tmp.gro
+    head -$(($N+2)) $NInputFile | tail -$N >> tmp.gro
+    tail -1 $NInputFile                    >> tmp.gro
+    mv tmp.gro W$N.gro
+    N=$N+1
+done
+declare -i N=$(($NInput+1))
+while [ $N -le $NEnd ]
+do
+    PrevN=$(($N-1))
+    head -1 $NInputFile                                        > tmp.gro
+    echo $N                                                   >> tmp.gro
+    head -$(($PrevN+2)) W$PrevN.gro | tail -$PrevN            >> tmp.gro
+    tail -2 W$PrevN.gro | head -1 | sed -e s/"$PrevN"W/"$N"W/ >> tmp.gro
+    tail -1 $NInputFile                                       >> tmp.gro
+    editconf -f tmp.gro -o W$N.gro
+    rm -f tmp.gro
+    rm -f \#*
+    N=$N+1
+done
+
+exit