From 9a2ec42910fcbe66a8b20b3609e9e52c671fa3f0 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 18 Jul 2011 19:30:13 +0200
Subject: [PATCH] Small cleanup in WholeMolecules
* Eliminated a possible tricky method to modify atom by relative index
* Eliminated duplicates in requested atom list
I also added a operators to AtomNumber, so it can be sorted with STL
algorithms
---
src/AtomNumber.h | 12 ++++++++++++
src/GenericWholeMolecules.cpp | 7 ++-----
2 files changed, 14 insertions(+), 5 deletions(-)
diff --git a/src/AtomNumber.h b/src/AtomNumber.h
index 65e17bc7d..5b55e4fdd 100644
--- a/src/AtomNumber.h
+++ b/src/AtomNumber.h
@@ -20,6 +20,8 @@ public:
void setIndex(unsigned);
static AtomNumber serial(unsigned);
static AtomNumber index(unsigned);
+ friend bool operator<(const AtomNumber&,const AtomNumber&);
+ friend bool operator==(const AtomNumber&,const AtomNumber&);
};
inline
@@ -62,6 +64,16 @@ AtomNumber AtomNumber::index(unsigned i){
return a;
}
+inline
+bool operator<(const AtomNumber&a,const AtomNumber&b){
+ return a.index_<b.index_;
+}
+
+inline
+bool operator==(const AtomNumber&a,const AtomNumber&b){
+ return a.index_==b.index_;
+}
+
}
diff --git a/src/GenericWholeMolecules.cpp b/src/GenericWholeMolecules.cpp
index bc35b9240..fead5982b 100644
--- a/src/GenericWholeMolecules.cpp
+++ b/src/GenericWholeMolecules.cpp
@@ -3,6 +3,7 @@
#include "ActionRegister.h"
#include "Vector.h"
#include "AtomNumber.h"
+#include "Tools.h"
#include <vector>
#include <string>
@@ -56,11 +57,6 @@ Vector & GenericWholeMolecules::modifyPosition(AtomNumber i){
return plumed.getAtoms().positions[i.index()];
}
-inline
-Vector & GenericWholeMolecules::modifyPosition(unsigned i){
- return plumed.getAtoms().positions[getAbsoluteIndex(i).index()];
-}
-
GenericWholeMolecules::GenericWholeMolecules(const ActionOptions&ao):
Action(ao),
ActionPilot(ao),
@@ -77,6 +73,7 @@ ActionAtomistic(ao)
merge.insert(merge.end(),group.begin(),group.end());
}
checkRead();
+ Tools::removeDuplicates(merge);
requestAtoms(merge);
}
--
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