From 9712bb9dafa961e3b5c7c4a80b035746d7db98e6 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Thu, 13 Jun 2013 11:37:23 +0100
Subject: [PATCH] Hid NL_STRIDE option in SecondaryStructure
---
src/secondarystructure/SecondaryStructureRMSD.cpp | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp
index 23b139c0b..06b8889ca 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.cpp
+++ b/src/secondarystructure/SecondaryStructureRMSD.cpp
@@ -55,7 +55,7 @@ void SecondaryStructureRMSD::registerKeywords( Keywords& keys ){
"However, if you are using some other option, then this cannot be used");
keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
keys.addFlag("VERBOSE",false,"write a more detailed output");
- keys.add("optional","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
+ keys.add("hidden","NL_STRIDE","the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities "
"that contributed less than TOL at the previous neighbor list update step are ignored.");
ActionWithVessel::registerKeywords( keys );
keys.use("LESS_THAN"); keys.use("MIN");
@@ -148,8 +148,11 @@ void SecondaryStructureRMSD::setSecondaryStructure( std::vector<Vector>& structu
}
if( secondary_rmsd.size()==0 && secondary_drmsd.size()==0 ){
- pos.resize( structure.size() );
- all_atoms.activateAll(); taskList.activateAll();
+ pos.resize( structure.size() ); taskList.activateAll();
+ for(unsigned i=0;i<taskList.getNumberActive();++i){
+ for(unsigned j=0;j<colvar_atoms[i].size();++j) all_atoms.activate( colvar_atoms[i][j] );
+ }
+ all_atoms.updateActiveMembers();
ActionAtomistic::requestAtoms( all_atoms.retrieveActiveList() );
forcesToApply.resize( getNumberOfDerivatives() );
--
GitLab