From cca21bb732fb6255bfb39276c0c1fa0204b5f516 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gt@eider.phy.qub.ac.uk>
Date: Mon, 20 Apr 2015 14:42:33 +0100
Subject: [PATCH] Fixed virial in PCARMSD
Also had to avoid using vector.clear with a std::vector<Vector> as
the code complains when the code is compiled with g++ and more
excessive debug options
---
src/colvar/PCARMSD.cpp | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/src/colvar/PCARMSD.cpp b/src/colvar/PCARMSD.cpp
index 2b37a229e..7cae2f76d 100644
--- a/src/colvar/PCARMSD.cpp
+++ b/src/colvar/PCARMSD.cpp
@@ -190,12 +190,11 @@ void PCARMSD::calculate(){
Value* value=getPntrToComponent(pca_names[i].c_str());
double val;val=0.;
for(unsigned iat=0;iat<getNumberOfAtoms();iat++){
- val+=dotProduct(alignedpos[iat]-centeredref[iat],eigenvectors[i][iat]);
+ val+=dotProduct(alignedpos[iat]-centeredref[iat],eigenvectors[i][iat]); der[iat].zero();
}
value->set(val);
// here the loop is reversed to better suit the structure of the derivative of the rotation matrix
double tmp1;
- der.clear();
for(unsigned a=0;a<3;a++){
for(unsigned b=0;b<3;b++){
for(unsigned iat=0;iat<getNumberOfAtoms();iat++){
@@ -217,7 +216,7 @@ void PCARMSD::calculate(){
}
}
- setBoxDerivativesNoPbc();
+ for(unsigned i=0;i<getNumberOfComponents();++i) setBoxDerivativesNoPbc( getPntrToComponent(i) );
}
--
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