Merge pull request #55 from camilafaccini/rollback

4comp rapid dilution files
softmaterialslab · Jan 30, 2024 · 2777aaf · 2777aaf
2 parents 17c59d2 + c350b04
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diff --git a/model_extension/4comp/rapid_dilution/parameter_sweep.sh b/model_extension/4comp/rapid_dilution/parameter_sweep.sh
@@ -0,0 +1,141 @@
+#!/bin/bash
+
+# EEE2+E2+Q2+K2 concentrations:  0.6 0.55 0.5 0.4 0.35 0.325 0.3 0.27 0.245 0.2 0.18 0.16 0.125 0.1 0.04
+
+# check the cutoff values below
+# double check everything
+
+for FOURCOMP in "EEE2E2Q2K2" 
+do
+if [ "$FOURCOMP" = "EEE2E2Q2K2" ]; then
+  echo "its EEE2 and E2 and Q2 and K2!"
+  USERVLP1="EEE2"
+  USERVLP2="E2"
+  USERVLP3="Q2"
+  USERVLP4="K2"
+  USERVLP1CHARGE="-2122"
+  USERSIGMAHC1RAW="5.16"
+  USERVLP2CHARGE="-1500"
+  USERSIGMAHC2RAW="5.16"
+  USERVLP3CHARGE="-1165"
+  USERSIGMAHC3RAW="4"
+  USERVLP4CHARGE="-622"
+  USERSIGMAHC4RAW="4"
+  for USERSALTCONC in 0.6 #0.55 0.5 0.4 0.35 0.325 0.3 0.27 0.245 0.2 0.18 0.16 0.125 0.1 0.04
+  do      
+    if [ "$USERSALTCONC" = 0.6 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0536841166259483"
+        USERVLPLinkerEScutoff="0.6045365500835798"
+        USERLinkerEScutoff="0.16092519609103764" 
+    elif [ "$USERSALTCONC" = 0.57 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0554699916420212"
+        USERVLPLinkerEScutoff="0.6061438375980455"
+        USERLinkerEScutoff="0.1621753086022888"     
+    elif [ "$USERSALTCONC" = 0.55 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0567201041532723"
+        USERVLPLinkerEScutoff="0.6072153626076892"
+        USERLinkerEScutoff="0.1632468336119326"     
+    elif [ "$USERSALTCONC" = 0.54 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0572558666580942"
+        USERVLPLinkerEScutoff="0.6077511251125112"
+        USERLinkerEScutoff="0.1636040086151472"     
+    elif [ "$USERSALTCONC" = 0.5 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0601132666838111"
+        USERVLPLinkerEScutoff="0.6100727626334062"
+        USERLinkerEScutoff="0.16574705863443487"     
+    elif [ "$USERSALTCONC" = 0.4 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0690426417641763"
+        USERVLPLinkerEScutoff="0.6177520252025201"
+        USERLinkerEScutoff="0.17253338369551238"     
+    elif [ "$USERSALTCONC" = 0.35 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0749360293172174"
+        USERVLPLinkerEScutoff="0.6227524752475248"
+        USERLinkerEScutoff="0.1771766587373023"     
+    elif [ "$USERSALTCONC" = 0.325 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0785077793493634"
+        USERVLPLinkerEScutoff="0.6257884627748488"
+        USERLinkerEScutoff="0.17967688375980453"     
+    elif [ "$USERSALTCONC" = 0.31 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0808294168702584"
+        USERVLPLinkerEScutoff="0.6277529252925291"
+        USERLinkerEScutoff="0.18146275877587756"     
+    elif [ "$USERSALTCONC" = 0.3 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.082436704384724"
+        USERVLPLinkerEScutoff="0.6291816253053877"
+        USERLinkerEScutoff="0.18271287128712868"     
+    elif [ "$USERSALTCONC" = 0.27 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0877943294329433"
+        USERVLPLinkerEScutoff="0.6338249003471775"
+        USERLinkerEScutoff="0.1868203838240967"     
+    elif [ "$USERSALTCONC" = 0.245 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.0931519544811623"
+        USERVLPLinkerEScutoff="0.6382895878873601"
+        USERLinkerEScutoff="0.19074930885945737"     
+    elif [ "$USERSALTCONC" = 0.2 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.1054744920920663"
+        USERVLPLinkerEScutoff="0.648826250482191"
+        USERLinkerEScutoff="0.1998572714414298"     
+    elif [ "$USERSALTCONC" = 0.18 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.112439404654751"
+        USERVLPLinkerEScutoff="0.654719638035232"
+        USERLinkerEScutoff="0.20503630898804162"     
+    elif [ "$USERSALTCONC" = 0.16 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.1206544297286871"
+        USERVLPLinkerEScutoff="0.6616845505979169"
+        USERLinkerEScutoff="0.21110828404268994"     
+    elif [ "$USERSALTCONC" = 0.125 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.1399418799022758"
+        USERVLPLinkerEScutoff="0.6781146007457888"
+        USERLinkerEScutoff="0.22521669666966695"     
+    elif [ "$USERSALTCONC" = 0.1 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.1597650925806866"
+        USERVLPLinkerEScutoff="0.6949018258968753"
+        USERLinkerEScutoff="0.23968228429985852"     
+    elif [ "$USERSALTCONC" = 0.04 ]; then
+        echo $USERSALTCONC
+        USERVLPEScutoff="1.2738825061077537"
+        USERVLPLinkerEScutoff="0.7909819017616047"
+        USERLinkerEScutoff="0.3196894850199306"     
+    fi        
+  dir="$USERVLP1"_"$USERVLP2"_"$USERVLP3"_"$USERVLP4"_c"$USERSALTCONC"
+  cp -a template/ $dir
+  cd $dir
+    sed -i 's/USERVLP1CHARGE/'$USERVLP1CHARGE'/g' in.4comp.template
+    sed -i 's/USERVLP2CHARGE/'$USERVLP2CHARGE'/g' in.4comp.template
+    sed -i 's/USERVLP3CHARGE/'$USERVLP3CHARGE'/g' in.4comp.template
+    sed -i 's/USERVLP4CHARGE/'$USERVLP4CHARGE'/g' in.4comp.template
+    sed -i 's/USERSIGMAHC1RAW/'$USERSIGMAHC1RAW'/g' in.4comp.template
+    sed -i 's/USERSIGMAHC2RAW/'$USERSIGMAHC2RAW'/g' in.4comp.template
+    sed -i 's/USERSIGMAHC3RAW/'$USERSIGMAHC3RAW'/g' in.4comp.template
+	sed -i 's/USERSIGMAHC4RAW/'$USERSIGMAHC4RAW'/g' in.4comp.template
+    sed -i 's/USERSALTCONC/'$USERSALTCONC'/g' in.4comp.template
+    sed -i 's/USERVLPEScutoff/'$USERVLPEScutoff'/g' in.4comp.template
+    sed -i 's/USERLinkerEScutoff/'$USERLinkerEScutoff'/g' in.4comp.template
+    sed -i 's/USERVLPLinkerEScutoff/'$USERVLPLinkerEScutoff'/g' in.4comp.template
+    sed -i 's/USERVLP1/'$USERVLP1'/g' assembly.pbs
+    sed -i 's/USERVLP2/'$USERVLP2'/g' assembly.pbs
+    sed -i 's/USERVLP3/'$USERVLP3'/g' assembly.pbs
+    sed -i 's/USERVLP4/'$USERVLP4'/g' assembly.pbs
+    sed -i 's/USERSALTCONC/'$USERSALTCONC'/g' assembly.pbs
+    sbatch assembly.pbs
+    cd ..
+  done
+fi
+done
diff --git a/model_extension/4comp/rapid_dilution/template/Makefile b/model_extension/4comp/rapid_dilution/template/Makefile
@@ -0,0 +1,10 @@
+clean:
+	rm -f *.log
+	rm -f log.lammps
+	rm thermo.dat
+
+dumpclean:
+	rm -f *.melt
+
+restartclean:
+	rm -f Restart*
diff --git a/model_extension/4comp/rapid_dilution/template/assembly.pbs b/model_extension/4comp/rapid_dilution/template/assembly.pbs
@@ -0,0 +1,16 @@
+#!/bin/bash
+#SBATCH [email protected]
+#SBATCH --nodes=1
+#SBATCH --ntasks-per-node=48
+#SBATCH --time=15:00:00
+#SBATCH -A r00312
+#SBATCH --partition=general
+#SBATCH --mail-type=FAIL,BEGIN,END
+#SBATCH --job-name=USERVLP1_USERVLP2_USERVLP3_USERVLP4_USERSALTCONC
+#SBATCH --output=out.log
+#SBATCH --error=err.log
+
+module load lammps/29Oct20
+
+cd      $SLURM_SUBMIT_DIR
+time srun -n 48 lmp_mpi < in.4comp.template
diff --git a/model_extension/4comp/rapid_dilution/template/cleanlog.sh b/model_extension/4comp/rapid_dilution/template/cleanlog.sh
@@ -0,0 +1,21 @@
+#!/bin/sh
+# the script below cleans up log.lammps to get thermo out
+file=log.lammps
+if test -s $file
+then
+awk '
+/Step/,/Loop/ { print }
+' $file > x.dat
+awk '
+!($0 ~ /Step/) { print }
+' x.dat > y.dat
+awk '
+!($0 ~ /Loop/) { print }
+' y.dat > thermo.dat
+rm x.dat
+rm y.dat
+echo "Generated thermo.dat"
+echo "Done!"
+else
+echo "where is log.lammps?"
+fi