From e9492f9d16b6afb3c4c86931d5c96db23f12ffc5 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sat, 27 Feb 2016 16:51:54 +0000
Subject: [PATCH] Ensured that PLUMED crashes with an error if user tries to
use too many atoms in multicolvar
---
src/multicolvar/MultiColvar.cpp | 16 ++-----------
src/multicolvar/MultiColvarBase.cpp | 30 ++++++++++++++-----------
src/multicolvar/MultiColvarBase.h | 2 ++
src/multicolvar/MultiColvarFunction.cpp | 13 ++---------
4 files changed, 23 insertions(+), 38 deletions(-)
diff --git a/src/multicolvar/MultiColvar.cpp b/src/multicolvar/MultiColvar.cpp
index 3a21f4520..b906e1a7a 100644
--- a/src/multicolvar/MultiColvar.cpp
+++ b/src/multicolvar/MultiColvar.cpp
@@ -102,20 +102,8 @@ void MultiColvar::readAtomsLikeKeyword( const std::string & key, int& natoms, st
t.resize(0);
}
if( all_atoms.size()>0 ){
- nblock=ablocks[0].size();
- if( natoms<4 ) resizeBookeepingArray( nblock, nblock );
-
- for(unsigned i=0;i<nblock;++i){
- if( natoms<4 ){
- unsigned cvcode=0, tmpc=1;
- for(unsigned j=0;j<natoms;++j){ cvcode += i*tmpc; tmpc *= nblock; }
- bookeeping(i,i).first=getFullNumberOfTasks();
- addTaskToList( cvcode );
- bookeeping(i,i).second=getFullNumberOfTasks();
- } else {
- addTaskToList( i );
- }
- }
+ nblock=0;
+ for(unsigned i=0;i<ablocks[0].size();++i) addTaskToList( i );
}
}
diff --git a/src/multicolvar/MultiColvarBase.cpp b/src/multicolvar/MultiColvarBase.cpp
index ff8a2478e..bac4526d1 100644
--- a/src/multicolvar/MultiColvarBase.cpp
+++ b/src/multicolvar/MultiColvarBase.cpp
@@ -67,7 +67,8 @@ ActionWithValue(ao),
ActionWithVessel(ao),
usepbc(false),
linkcells(comm),
-usespecies(false)
+usespecies(false),
+nblock(0)
{
if( keywords.exists("NOPBC") ){
bool nopbc=!usepbc; parseFlag("NOPBC",nopbc);
@@ -90,13 +91,16 @@ void MultiColvarBase::resizeBookeepingArray( const unsigned& num1, const unsigne
void MultiColvarBase::setupMultiColvarBase(){
// Setup decoder array
- if( !usespecies && ablocks.size()<4 ){
+ if( !usespecies && nblock>0 ){
+ // Check if number of atoms is too large
+ if( pow( nblock, ablocks.size()+1)>std::numeric_limits<unsigned>::max() ) error("number of atoms in groups is too big for PLUMED to handle");
+
decoder.resize( ablocks.size() ); unsigned code=1;
for(unsigned i=0;i<ablocks.size();++i){ decoder[ablocks.size()-1-i]=code; code *= nblock; }
- use_for_central_atom.resize( ablocks.size(), true );
+ ncentral=ablocks.size(); use_for_central_atom.resize( ablocks.size(), true );
numberForCentralAtom = 1.0 / static_cast<double>( ablocks.size() );
} else if( !usespecies ){
- use_for_central_atom.resize( ablocks.size(), true );
+ ncentral=ablocks.size(); use_for_central_atom.resize( ablocks.size(), true );
numberForCentralAtom = 1.0 / static_cast<double>( ablocks.size() );
}
@@ -110,7 +114,8 @@ void MultiColvarBase::setAtomsForCentralAtom( const std::vector<bool>& catom_ind
use_for_central_atom[i]=catom_ind[i];
if( use_for_central_atom[i] ) nat++;
}
- plumed_dbg_assert( nat>0 ); numberForCentralAtom = 1.0 / static_cast<double>( nat );
+ plumed_dbg_assert( nat>0 ); ncentral=nat;
+ numberForCentralAtom = 1.0 / static_cast<double>( nat );
}
void MultiColvarBase::turnOnDerivatives(){
@@ -125,7 +130,7 @@ void MultiColvarBase::setLinkCellCutoff( const double& lcut ){
}
void MultiColvarBase::setupLinkCells(){
- if( !linkcells.enabled() ) return ;
+ if( (!usespecies && nblock==0) || !linkcells.enabled() ) return ;
unsigned iblock;
if( usespecies ){
@@ -234,7 +239,7 @@ void MultiColvarBase::setupLinkCells(){
}
void MultiColvarBase::decodeIndexToAtoms( const unsigned& taskCode, std::vector<unsigned>& atoms ) const {
- plumed_dbg_assert( atoms.size()==ablocks.size() && !usespecies && ablocks.size()<4 );
+ plumed_dbg_assert( atoms.size()==ablocks.size() && !usespecies && nblock>0 );
unsigned scode = taskCode;
for(unsigned i=0;i<ablocks.size();++i){
unsigned ind=( scode / decoder[i] );
@@ -248,7 +253,7 @@ bool MultiColvarBase::setupCurrentAtomList( const unsigned& taskCode, AtomValueP
if( isDensity() ) return true;
unsigned natomsper=myatoms.setupAtomsFromLinkCells( taskCode, getPositionOfAtomForLinkCells(taskCode), linkcells );
return natomsper>1;
- } else if( ablocks.size()<4 ){
+ } else if( nblock>0 ){
std::vector<unsigned> atoms( ablocks.size() );
decodeIndexToAtoms( taskCode, atoms ); myatoms.setNumberOfAtoms( ablocks.size() );
for(unsigned i=0;i<ablocks.size();++i) myatoms.setAtom( i, atoms[i] );
@@ -292,7 +297,7 @@ Vector MultiColvarBase::getCentralAtomPos( const unsigned& taskIndex ){
if( usespecies || isDensity() ){
return getPositionOfAtomForLinkCells(curr);
- } else if( ablocks.size()<4 ){
+ } else if( nblock>0 ){
// double factor=1.0/static_cast<double>( ablocks.size() );
Vector mypos; mypos.zero();
std::vector<unsigned> atoms( ablocks.size() ); decodeIndexToAtoms( curr, atoms );
@@ -317,9 +322,8 @@ CatomPack MultiColvarBase::getCentralAtomPack( const unsigned& basn, const unsig
mypack.resize(1);
mypack.setIndex( 0, basn + curr );
mypack.setDerivative( 0, Tensor::identity() );
- } else if( ablocks.size()<4 ){
- mypack.resize(ablocks.size());
- unsigned k=0;
+ } else if( nblock>0 ){
+ mypack.resize(ncentral); unsigned k=0;
std::vector<unsigned> atoms( ablocks.size() ); decodeIndexToAtoms( curr, atoms );
for(unsigned i=0;i<ablocks.size();++i){
if( use_for_central_atom[i] ){
@@ -329,7 +333,7 @@ CatomPack MultiColvarBase::getCentralAtomPack( const unsigned& basn, const unsig
}
}
} else {
- unsigned k=0;
+ mypack.resize(ncentral); unsigned k=0;
for(unsigned i=0;i<ablocks.size();++i){
if( use_for_central_atom[i] ){
mypack.setIndex( k, basn + ablocks[i][curr] );
diff --git a/src/multicolvar/MultiColvarBase.h b/src/multicolvar/MultiColvarBase.h
index 227e9ef6e..c47c89b38 100644
--- a/src/multicolvar/MultiColvarBase.h
+++ b/src/multicolvar/MultiColvarBase.h
@@ -56,6 +56,8 @@ private:
LinkCells linkcells;
/// This remembers where the boundaries are for the tasks. It makes link cells work fast
Matrix<std::pair<unsigned,unsigned> > bookeeping;
+/// Number of atoms that are being used for central atom position
+ unsigned ncentral;
/// Bool vector telling us which atoms are required to calculate central atom position
std::vector<bool> use_for_central_atom;
/// 1/number of atoms involved in central atoms
diff --git a/src/multicolvar/MultiColvarFunction.cpp b/src/multicolvar/MultiColvarFunction.cpp
index cbcd2aa8c..da48b45d1 100644
--- a/src/multicolvar/MultiColvarFunction.cpp
+++ b/src/multicolvar/MultiColvarFunction.cpp
@@ -129,23 +129,14 @@ void MultiColvarFunction::buildSets(){
if( mybasemulticolvars[i]->getFullNumberOfTasks()!=nblock ){
error("mismatch between numbers of tasks in various base multicolvars");
}
-// mybasemulticolvars[i]->buildDataStashes( false, 0.0 );
}
- ablocks.resize( mybasemulticolvars.size() );
+ nblock=0; ablocks.resize( mybasemulticolvars.size() );
usespecies=false; // current_atoms.resize( mybasemulticolvars.size() );
for(unsigned i=0;i<mybasemulticolvars.size();++i){
ablocks[i].resize( nblock );
for(unsigned j=0;j<nblock;++j) ablocks[i][j]=i*nblock+j;
}
- for(unsigned i=0;i<nblock;++i){
- if( mybasemulticolvars.size()<4 ){
- unsigned cvcode=0, tmpc=1;
- for(unsigned j=0;j<ablocks.size();++j){ cvcode +=i*tmpc; tmpc *= nblock; }
- addTaskToList( cvcode );
- } else {
- addTaskToList( i );
- }
- }
+ for(unsigned i=0;i<nblock;++i) addTaskToList( i );
setupAtomLists();
}
--
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