From 315e67461312a4cf1cad5e635292617b0d6d4ab7 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 5 Feb 2018 19:40:08 +0100
Subject: [PATCH] Fixed #337
Fixed partial_tempering with gromacs 5 convention. Old behavior can be
forced with --gromacs4 option.
---
scripts/partial_tempering.sh | 67 ++++++++++++++++++++++++------------
1 file changed, 45 insertions(+), 22 deletions(-)
diff --git a/scripts/partial_tempering.sh b/scripts/partial_tempering.sh
index e3dc15dcf..2e5f1832b 100755
--- a/scripts/partial_tempering.sh
+++ b/scripts/partial_tempering.sh
@@ -1,3 +1,4 @@
+# vim:ft=awk
if [ "$1" = --description ] ; then
echo "create a new collective variable from a template"
exit 0
@@ -7,7 +8,7 @@ if [ "$1" = --help ] || [ "$1" = -h ] ; then
cat <<EOF
Usage:
- plumed partial_tempering scale < processed.top
+ plumed partial_tempering [--gromacs4] scale < processed.top
where scale is the Hamiltonian scaling factor and
processed.top is a post-processed topology file (i.e. produced with grompp -pp)
@@ -55,7 +56,14 @@ EOF
exit
fi
-awk -v scale=$1 '
+gromacs5=1
+
+if [ $1 == --gromacs4 ] ; then
+ gromacs5=0
+ shift
+fi
+
+awk -v scale=$1 -v gromacs5=$gromacs5 '
BEGIN{
combrule=1;
}
@@ -73,6 +81,39 @@ function warning(msg)
{
print "WARNING:",msg | "cat 1>&2"
}
+function find_matching_torsion(params,atype, a1,a2,a3,a4,iswitch,progression,test,array,param,countX,bestCountX,bestMatch)
+{
+ progression=NR
+ bestCountX=5
+ for(iswitch=0;iswitch<32;iswitch++){
+ countX=0
+ if(iswitch%2==0){
+ a1=atype[1]; a2=atype[2]; a3=atype[3]; a4=atype[4];
+ } else {
+ a1=atype[4]; a2=atype[3]; a3=atype[2]; a4=atype[1];
+ }
+ if(int(iswitch/2)%2==1){ a1="X"; countX++; }
+ if(int(iswitch/4)%2==1){ a2="X"; countX++; }
+ if(int(iswitch/8)%2==1){ a3="X"; countX++; }
+ if(int(iswitch/16)%2==1){a4="X"; countX++; }
+ test=a1"-"a2"-"a3"-"a4"-"$5;
+ if(test in params){
+ split(params[test],array,":");
+ bestMatch=0;
+ if(gromacs5) {
+ if(countX<bestCountX || (countX==bestCountX && array[1]<progression)) bestMatch=1
+ } else {
+ if(array[1]<progression) bestMatch=1;
+ }
+ if(bestMatch){
+ progression=array[1];
+ bestCountX=countX
+ param=params[test];
+ }
+ }
+ }
+ return param;
+}
{
# This is the suffix for "hot" atoms:
suffix="_";
@@ -185,27 +226,9 @@ function warning(msg)
atype[2]=bondtype[ato[$2]]
atype[3]=bondtype[ato[$3]]
atype[4]=bondtype[ato[$4]]
+
+ param=find_matching_torsion(params,atype);
- progression=NR
- for(iswitch=0;iswitch<32;iswitch++){
- if(iswitch%2==0){
- a1=atype[1]; a2=atype[2]; a3=atype[3]; a4=atype[4];
- } else {
- a1=atype[4]; a2=atype[3]; a3=atype[2]; a4=atype[1];
- }
- if(int(iswitch/2)%2==1) a1="X";
- if(int(iswitch/4)%2==1) a2="X";
- if(int(iswitch/8)%2==1) a3="X";
- if(int(iswitch/16)%2==1) a4="X";
- test=a1"-"a2"-"a3"-"a4"-"$5;
- if(test in params){
- split(params[test],array,":");
- if(array[1]<progression){
- progression=array[1];
- param=params[test];
- }
- }
- }
n=split(param,array,":");
if(n<=1) error("params not found "$1" "$2" "$3" "$4" "$5" "atype[1]" "atype[2]" "atype[3]" "atype[4]);
--
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