From 8eb6402dc2e264dfa5a1c8089da58e360e8db02b Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Thu, 13 Jun 2013 00:12:02 +0200
Subject: [PATCH] Made fast RMSD the default when possible (align==displace)
---
src/tools/RMSD.cpp | 11 -----------
1 file changed, 11 deletions(-)
diff --git a/src/tools/RMSD.cpp b/src/tools/RMSD.cpp
index 4ec6e05cf..63878a1bd 100644
--- a/src/tools/RMSD.cpp
+++ b/src/tools/RMSD.cpp
@@ -145,17 +145,6 @@ double RMSD::calculate(const std::vector<Vector> & positions,std::vector<Vector>
bool fastversion=true;
// this is because fast version only works with align==displace
if (align!=displace) fastversion=false;
- // this is because of an inconsistent usage of weights in different versions:
- unsigned i;
- for(i=0;i<align.size();i++){
- if(align[i]!=0.0) break;
- }
- for(unsigned j=i+1;j<align.size();j++){
- if(align[i]!=align[j] && align[j]!=0.0){
- fastversion=false;
- break;
- }
- }
if (fastversion){
// this is the fast routine but in the "safe" mode, which gives less numerical error:
ret=optimalAlignment<true>(align,displace,positions,reference,derivatives,squared);
--
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