Added inverse tension functions for speed. Bumped to version 0.7.

[sawsim.git] / testing / bell_rate / run_test.sh

diff --git a/testing/bell_rate/run_test.sh b/testing/bell_rate/run_test.sh
index 931eeba43eea0fb9a6680acbd5c17052eb432406..78421ca86a0703c32633c824398ff8b06c5a0bcf 100755 (executable)
--- a/testing/bell_rate/run_test.sh
+++ b/testing/bell_rate/run_test.sh
@@ -26,13 +26,17 @@
 #   The histogram scaling isn't dD/df, though, it's dD/d(bin)
 #        dD/d(bin) = dD/df df/d(bin) = binwidth P0 z e^{bf + z/b(1-e^{bf})}
 #
-#   test with lots of runs of           v-dx=1
-#     sawsim -v1 -mhooke -a1 -kbell -K1,1 -T7.24296e22 -F1
-#              ^- v=1      ^- k=1     ^-a=1 ^-1/kB
+#   test with lots of runs of
+#              v- T=1/kB    v- v=1            v- k=1
+#     sawsim -T7.24296e22 -v1 -s folded,hooke,1 -N1 -s unfolded,null \
+#         -k "folded,unfolded,bell,{1,1}" -q folded
+#                                   ^- {a,dx}={1,1}
 #   (kB = 1.3806503 10-23 J/K, we use T=1/kB to get the bell K=e^{-f})
 #
-#   70 runs of that takes ~1 second:
-#     time xtimes 200 sawsim -v1 -mhooke -a1 -kconst -K1 -F1 > /dev/null
+#   60 runs of that takes ~1 second:
+#     time xtimes 60 sawsim -T7.24296e22 -v1 -s folded,hooke,1 -N1 \
+#         -s unfolded,null -k "folded,unfolded,bell,{1,1}" -q folded \
+#         > /dev/null
 #
 # usage: bell_rate.sh
 
@@ -49,6 +53,7 @@ PNGFILE=bell_rate.png
 #   dD/d(bin) = binwidth P0 z e^{bf + z/b(1-e^{bf})}
 # where z ≡ a/kv, and b = Δx/kBT
 KB=1.3806503e-23 # J/K
+#STYLE="ones"
 STYLE="protein"
 if [ "$STYLE" == "ones" ]
 then
@@ -74,9 +79,15 @@ THEORY_FN="$df * $N * $Z * exp($B*x + $Z/$B *(1 - exp($B*x)))"
 > $DATA
 if [ "$ISACLUSTER" -eq 1 ]
 then
-    qcmd "xtimes $N $SAWSIM -v$V -mhooke -a$K -kbell -K$A,$DX -T$T -F1 | grep -v '^#' >> $DATA"
+    # Sawsim <= 0.5
+    #qcmd "xtimes $N $SAWSIM -T$T -v$V -mhooke -a$K -kbell -K$A,$DX -F1 | grep -v '^#' >> $DATA"
+    # Sawsim >= 0.6
+    qcmd "xtimes $N $SAWSIM -T$T -v$V -s folded,hooke,$K -N1 -s unfolded,null -k 'folded,unfolded,bell,{$A,$DX}' -q folded | grep -v '^#' | cut -f1 >> $DATA"
 else
-    xtimes $N $SAWSIM -v$V -mhooke -a$K -kbell -K$A,$DX -T$T -F1 | grep -v '^#' >> $DATA
+    # Sawsim <= 0.5
+    #xtimes $N $SAWSIM -T$T -v$V -mhooke -a$K -kbell -K$A,$DX -F1 | grep -v '^#' >> $DATA
+    # Sawsim >= 0.6
+    xtimes $N $SAWSIM -T$T -v$V -s folded,hooke,$K -N1 -s unfolded,null -k "folded,unfolded,bell,{$A,$DX}" -q folded | grep -v '^#' | cut -f1 >> $DATA
 fi
 
 # histogram the data
@@ -87,7 +98,7 @@ FIT=`cat $HIST | ./fit_bell`
 #echo "$FIT"
 FITZ=`echo "$FIT" | sed -n 's/a:[[:space:]]*//p'`
 FITB=`echo "$FIT" | sed -n 's/b:[[:space:]]*//p'`
-echo -e "a:\t$FITZ\t(expected $Z)"
+echo -e "z:\t$FITZ\t(expected $Z)"
 echo -e "b:\t$FITB\t(expected $B)"
 
 # generate gnuplot script