From e49cba3a5b4dbb296db7f9f21227c7b1b51e3300 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Thu, 12 Dec 2013 07:32:19 +0000
Subject: [PATCH] Fixed a bug in multicolvar that appears when base cvs use
many atoms
---
src/multicolvar/MultiColvar.cpp | 10 +++++++---
src/multicolvar/MultiColvarBase.cpp | 14 ++++++++------
2 files changed, 15 insertions(+), 9 deletions(-)
diff --git a/src/multicolvar/MultiColvar.cpp b/src/multicolvar/MultiColvar.cpp
index 72af3386b..7449a90b0 100644
--- a/src/multicolvar/MultiColvar.cpp
+++ b/src/multicolvar/MultiColvar.cpp
@@ -98,9 +98,13 @@ void MultiColvar::readAtomsLikeKeyword( const std::string & key, int& natoms ){
if( all_atoms.fullSize()>0 ){
current_atoms.resize( natoms ); nblock=ablocks[0].size();
for(unsigned i=0;i<nblock;++i){
- unsigned cvcode=0, tmpc=1;
- for(unsigned j=0;j<natoms;++j){ cvcode += i*tmpc; tmpc *= nblock; }
- addTaskToList( cvcode );
+ if( natoms<4 ){
+ unsigned cvcode=0, tmpc=1;
+ for(unsigned j=0;j<natoms;++j){ cvcode += i*tmpc; tmpc *= nblock; }
+ addTaskToList( cvcode );
+ } else {
+ addTaskToList( i );
+ }
}
}
}
diff --git a/src/multicolvar/MultiColvarBase.cpp b/src/multicolvar/MultiColvarBase.cpp
index 9f2d6c216..d609ed732 100644
--- a/src/multicolvar/MultiColvarBase.cpp
+++ b/src/multicolvar/MultiColvarBase.cpp
@@ -81,11 +81,10 @@ void MultiColvarBase::copyActiveAtomsToFunction( MultiColvarBase* myfunction, co
void MultiColvarBase::setupMultiColvarBase(){
// Setup decoder array
- if( !usespecies ){
+ if( !usespecies && ablocks.size()<4 ){
decoder.resize( ablocks.size() ); unsigned code=1;
for(unsigned i=0;i<ablocks.size();++i){ decoder[ablocks.size()-1-i]=code; code *= nblock; }
- } else if( ablocks.size()>0 ) {
- plumed_assert( ablocks.size()==1 );
+ } else if( ablocks.size()==1 ) {
// Setup coordination sphere
csphere_atoms.resize( getFullNumberOfTasks() ); unsigned nflags=0;
for(unsigned i=0;i<getFullNumberOfTasks();++i){
@@ -97,7 +96,7 @@ void MultiColvarBase::setupMultiColvarBase(){
csphere_atoms[i].activateAll();
}
csphere_flags.resize( nflags, 0 );
- }
+ }
// Do an initial task list update
finishTaskListUpdate();
// Setup underlying ActionWithVessel
@@ -158,7 +157,7 @@ bool MultiColvarBase::setupCurrentAtomList( const unsigned& taskCode ){
}
}
if( natomsper==1 ) return isDensity();
- } else {
+ } else if( current_atoms.size()<4 ){
natomsper=current_atoms.size();
unsigned scode = taskCode;
for(unsigned i=0;i<ablocks.size();++i){
@@ -166,7 +165,10 @@ bool MultiColvarBase::setupCurrentAtomList( const unsigned& taskCode ){
current_atoms[i]=getBaseQuantityIndex( ablocks[i][ind] );
scode -= ind*decoder[i];
}
- }
+ } else {
+ natomsper=current_atoms.size();
+ for(unsigned i=0;i<ablocks.size();++i) current_atoms[i]=getBaseQuantityIndex( ablocks[i][taskCode] );
+ }
return true;
}
--
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