From e5cd991bfa51a4265683933728e04d27f0fae58f Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sun, 16 Nov 2014 09:50:44 +0000
Subject: [PATCH] All vessel::calculate functions are now const
---
src/crystallization/DFSClustering.cpp | 4 +-
src/crystallization/GradientVessel.cpp | 30 +--
src/crystallization/VectorMean.cpp | 4 +-
src/crystallization/VectorSum.cpp | 4 +-
src/mapping/SpathVessel.cpp | 4 +-
src/mapping/ZpathVessel.cpp | 4 +-
.../BridgedMultiColvarFunction.cpp | 42 +---
src/vesselbase/ActionWithVessel.cpp | 39 ++--
src/vesselbase/ActionWithVessel.h | 4 +-
src/vesselbase/Between.cpp | 2 +-
src/vesselbase/Between.h | 2 +-
src/vesselbase/BridgeVessel.cpp | 12 +-
src/vesselbase/BridgeVessel.h | 11 +-
src/vesselbase/FunctionVessel.cpp | 4 +-
src/vesselbase/FunctionVessel.h | 6 +-
src/vesselbase/LessThan.cpp | 2 +-
src/vesselbase/LessThan.h | 2 +-
src/vesselbase/Max.cpp | 4 +-
src/vesselbase/Mean.cpp | 4 +-
src/vesselbase/Min.cpp | 4 +-
src/vesselbase/MoreThan.cpp | 4 +-
src/vesselbase/ShortcutVessel.h | 2 +-
src/vesselbase/StoreDataVessel.cpp | 199 ++++--------------
src/vesselbase/StoreDataVessel.h | 114 ++--------
src/vesselbase/Sum.cpp | 4 +-
src/vesselbase/Vessel.h | 6 +-
26 files changed, 139 insertions(+), 378 deletions(-)
diff --git a/src/crystallization/DFSClustering.cpp b/src/crystallization/DFSClustering.cpp
index 26f5e7aa1..174ebb443 100644
--- a/src/crystallization/DFSClustering.cpp
+++ b/src/crystallization/DFSClustering.cpp
@@ -150,7 +150,7 @@ void DFSClustering::completeCalculation(){
ActionWithVessel::doJobsRequiredBeforeTaskList(); // Note we loose adjacency data by doing this
// Get size for buffer
unsigned bsize=0; std::vector<double> buffer( getSizeOfBuffer( bsize ), 0.0 );
- std::vector<double> vals( getNumberOfQuantities() );
+ std::vector<double> vals( getNumberOfQuantities() ); std::vector<unsigned> der_index;
vesselbase::MultiValue myvals( getNumberOfQuantities(), getNumberOfDerivatives() );
vesselbase::MultiValue bvals( getNumberOfQuantities(), getNumberOfDerivatives() );
// Get rid of bogus derivatives
@@ -163,7 +163,7 @@ void DFSClustering::completeCalculation(){
for(unsigned i=0;i<vals.size();++i) myvals.setValue( i, vals[i] );
if( !doNotCalculateDerivatives() ) getVectorDerivatives( i, false, myvals );
// Run calculate all vessels
- calculateAllVessels( i, myvals, bvals, buffer );
+ calculateAllVessels( i, myvals, bvals, buffer, der_index );
myvals.clearAll();
}
// MPI Gather everything
diff --git a/src/crystallization/GradientVessel.cpp b/src/crystallization/GradientVessel.cpp
index 0f2d6372d..fbbb2adbc 100644
--- a/src/crystallization/GradientVessel.cpp
+++ b/src/crystallization/GradientVessel.cpp
@@ -34,15 +34,13 @@ private:
bool isdens;
unsigned nweights, ncomponents;
std::vector<unsigned> starts;
-// std::vector<double> val_interm;
-// Matrix<double> der_interm;
public:
static void registerKeywords( Keywords& keys );
static void reserveKeyword( Keywords& keys );
GradientVessel( const vesselbase::VesselOptions& da );
std::string function_description();
void resize();
- bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer );
+ bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
void finish( const std::vector<double>& buffer );
};
@@ -68,7 +66,6 @@ FunctionVessel(da)
} else {
ncomponents = 1;
}
- // ncomponents = vg->vend;
starts.push_back(0);
if( vg->nbins[0]>0 ){
@@ -96,34 +93,26 @@ void GradientVessel::resize(){
unsigned nder=getAction()->getNumberOfDerivatives();
resizeBuffer( (1+nder)*(ncomponents+1)*nweights );
setNumberOfDerivatives( nder );
-// val_interm.resize( ncomponents*nweights );
-// der_interm.resize( ncomponents*nweights, nder );
} else {
setNumberOfDerivatives(0);
resizeBuffer( (ncomponents+1)*nweights );
-// val_interm.resize( ncomponents*nweights );
}
}
-bool GradientVessel::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer ){
+bool GradientVessel::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
unsigned nder=getAction()->getNumberOfDerivatives();
unsigned wstart, cstart; if( ncomponents==1 ){ cstart=1; wstart=2; } else { cstart=2; wstart=2+ncomponents; }
for(unsigned iw=0;iw<nweights;++iw){
unsigned xx = (ncomponents+1)*iw;
- double weight=myvals.get(wstart+iw); // getAction()->getElementValue(ncomponents + iw);
+ double weight=myvals.get(wstart+iw);
buffer[bufstart+xx*(nder+1)] += weight;
myvals.chainRule( wstart + iw, xx, 1, 0, 1.0, bufstart, buffer );
- // addValueIgnoringTolerance( xx, weight );
- // getAction()->chainRuleForElementDerivatives( xx , ncomponents + iw, 1.0, bufstart, buffer );
for(unsigned jc=0;jc<ncomponents;++jc){
- double colvar=myvals.get( cstart + jc ); // getAction()->getElementValue( jc );
- // addValueIgnoringTolerance( xx + 1 + jc, weight*colvar );
+ double colvar=myvals.get( cstart + jc );
buffer[bufstart+(xx+1+jc)*(nder+1) ] += weight*colvar;
myvals.chainRule( cstart + jc, xx + 1 + jc, 1, 0, weight, bufstart, buffer );
myvals.chainRule( wstart + iw, xx + 1 + jc, 1, 0, colvar, bufstart, buffer );
- // getAction()->chainRuleForElementDerivatives( xx + 1 + jc, jc, weight, bufstart, buffer );
- // getAction()->chainRuleForElementDerivatives( xx + 1 + jc, ncomponents + iw, colvar, bufstart, buffer );
}
}
@@ -137,25 +126,24 @@ void GradientVessel::finish( const std::vector<double>& buffer ){
if( isdens ){
for(unsigned iw=0;iw<nweights;++iw){
- val_interm[iw] = buffer[bufstart + 2*iw*(1+nder)]; // getFinalValue( 2*iw );
+ val_interm[iw] = buffer[bufstart + 2*iw*(1+nder)];
if( getAction()->derivativesAreRequired() ){
unsigned wstart = bufstart + 2*iw*(nder+1) + 1;
- for(unsigned jder=0;jder<nder;++jder) der_interm( iw, jder ) += buffer[ wstart + jder ]; // getBufferElement( wstart + jder );
+ for(unsigned jder=0;jder<nder;++jder) der_interm( iw, jder ) += buffer[ wstart + jder ];
}
}
} else {
for(unsigned iw=0;iw<nweights;++iw){
unsigned xx = (ncomponents+1)*iw;
- double ww=buffer[bufstart + xx*(1+nder)]; // getFinalValue( xx );
- for(unsigned jc=0;jc<ncomponents;++jc) val_interm[ iw*ncomponents + jc ] = buffer[bufstart + (xx+1+jc)*(1+nder)] / ww; //getFinalValue( xx + 1 + jc ) / ww;
+ double ww=buffer[bufstart + xx*(1+nder)];
+ for(unsigned jc=0;jc<ncomponents;++jc) val_interm[ iw*ncomponents + jc ] = buffer[bufstart + (xx+1+jc)*(1+nder)] / ww;
if( getAction()->derivativesAreRequired() ){
unsigned wstart = bufstart + xx*(nder+1) + 1;
for(unsigned jc=0;jc<ncomponents;++jc){
unsigned bstart = bufstart + ( xx + 1 + jc )*(nder+1) + 1;
- double val = buffer[bufstart + (nder+1)*(xx+1+jc)]; // getFinalValue( xx + 1 + jc );
+ double val = buffer[bufstart + (nder+1)*(xx+1+jc)];
for(unsigned jder=0;jder<nder;++jder)
der_interm( iw*ncomponents + jc, jder ) = (1.0/ww)*buffer[bstart + jder] - (val/(ww*ww))*buffer[wstart + jder];
- // (1.0/ww)*getBufferElement( bstart + jder ) - (val/(ww*ww))*getBufferElement( wstart + jder );
}
}
}
diff --git a/src/crystallization/VectorMean.cpp b/src/crystallization/VectorMean.cpp
index 64c192701..965ab55eb 100644
--- a/src/crystallization/VectorMean.cpp
+++ b/src/crystallization/VectorMean.cpp
@@ -35,7 +35,7 @@ public:
VectorMean( const vesselbase::VesselOptions& da );
std::string function_description();
void resize();
- bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer );
+ bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
void finish( const std::vector<double>& buffer );
};
@@ -73,7 +73,7 @@ void VectorMean::resize(){
}
}
-bool VectorMean::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer ){
+bool VectorMean::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
unsigned ncomp=getAction()->getNumberOfQuantities()-2, nder=getAction()->getNumberOfDerivatives();
double weight=myvals.get(0); plumed_dbg_assert( weight>=getTolerance() );
diff --git a/src/crystallization/VectorSum.cpp b/src/crystallization/VectorSum.cpp
index f12e098f9..1c6b3bf7d 100644
--- a/src/crystallization/VectorSum.cpp
+++ b/src/crystallization/VectorSum.cpp
@@ -35,7 +35,7 @@ public:
VectorSum( const vesselbase::VesselOptions& da );
std::string function_description();
void resize();
- bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer );
+ bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
void finish( const std::vector<double>& buffer );
};
@@ -73,7 +73,7 @@ void VectorSum::resize(){
}
}
-bool VectorSum::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer ){
+bool VectorSum::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
unsigned ncomp=getAction()->getNumberOfQuantities()-2, nder=getAction()->getNumberOfDerivatives();
double weight=myvals.get(0);
diff --git a/src/mapping/SpathVessel.cpp b/src/mapping/SpathVessel.cpp
index 525244eb2..2ca3ad40c 100644
--- a/src/mapping/SpathVessel.cpp
+++ b/src/mapping/SpathVessel.cpp
@@ -38,7 +38,7 @@ public:
SpathVessel( const vesselbase::VesselOptions& da );
std::string function_description();
void prepare();
- bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer );
+ bool calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_index ) const ;
};
PLUMED_REGISTER_VESSEL(SpathVessel,"SPATH")
@@ -74,7 +74,7 @@ void SpathVessel::prepare(){
foundoneclose=false;
}
-bool SpathVessel::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer ){
+bool SpathVessel::calculate( const unsigned& current, vesselbase::MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_index ) const {
double pp=mymap->getPropertyValue( current, mycoordnumber ), weight=myvals.get(0);
if( weight<getTolerance() ) return false;
buffer[bufstart] += weight*pp; buffer[bufstart+1+nderiv] += weight;
diff --git a/src/mapping/ZpathVessel.cpp b/src/mapping/ZpathVessel.cpp
index c5ee11d54..b22e89f1a 100644
--- a/src/mapping/ZpathVessel.cpp
+++ b/src/mapping/ZpathVessel.cpp
@@ -34,7 +34,7 @@ public:
static void reserveKeyword( Keywords& keys );
ZpathVessel( const vesselbase::VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
double finalTransform( const double& val, double& dv );
};
@@ -61,7 +61,7 @@ std::string ZpathVessel::function_description(){
return "the distance from the low-dimensional manifold";
}
-double ZpathVessel::calcTransform( const double& val, double& dv ){
+double ZpathVessel::calcTransform( const double& val, double& dv ) const {
dv=0.0; return 1.0;
}
diff --git a/src/multicolvar/BridgedMultiColvarFunction.cpp b/src/multicolvar/BridgedMultiColvarFunction.cpp
index 1cdb192ef..6b82ce322 100644
--- a/src/multicolvar/BridgedMultiColvarFunction.cpp
+++ b/src/multicolvar/BridgedMultiColvarFunction.cpp
@@ -51,10 +51,6 @@ MultiColvarBase(ao)
for(unsigned i=0;i<mycolv->getFullNumberOfTasks();++i) addTaskToList( mycolv->getTaskCode(i) );
}
-//void BridgedMultiColvarFunction::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ){
-// mycolv->getIndexList( ntotal, jstore, maxder, indices );
-//}
-
void BridgedMultiColvarFunction::transformBridgedDerivatives( const unsigned& current, vesselbase::MultiValue& invals, vesselbase::MultiValue& outvals ){
completeTask( current, invals, outvals );
@@ -70,44 +66,12 @@ void BridgedMultiColvarFunction::transformBridgedDerivatives( const unsigned& cu
outvals.sortActiveList();
}
-/// These two functions (commented out one underneath) are needed and are a bit tricky
void BridgedMultiColvarFunction::performTask( const unsigned& taskIndex, const unsigned& current, vesselbase::MultiValue& myvals ){
- //atoms_with_derivatives.deactivateAll();
-
- // GAT this is for recomputing - this needs to work -- how?
- if( !myBridgeVessel->prerequisitsCalculated() ){
- mycolv->performTask( taskIndex, current, myvals );
- }
-
- // completeTask( myvals, outvals ); -- also need this
- //atoms_with_derivatives.updateActiveMembers();
+ vesselbase::MultiValue invals( mycolv->getNumberOfQuantities(), mycolv->getNumberOfDerivatives() );
+ mycolv->performTask( taskIndex, current, invals );
+ transformBridgedDerivatives( taskIndex, invals, myvals );
}
-// Vector BridgedMultiColvarFunction::retrieveCentralAtomPos(){
-// if( atomsWithCatomDer.getNumberActive()==0 ){
-// Vector cvec = mycolv->retrieveCentralAtomPos();
-//
-// // Copy the value and derivatives from the MultiColvar
-// atomsWithCatomDer.emptyActiveMembers();
-// for(unsigned i=0;i<3;++i){
-// setElementValue( getCentralAtomElementIndex() + i, mycolv->getElementValue( mycolv->getCentralAtomElementIndex() + i ) );
-// unsigned nbase = ( getCentralAtomElementIndex() + i)*getNumberOfDerivatives();
-// unsigned nbas2 = ( mycolv->getCentralAtomElementIndex() + i )*mycolv->getNumberOfDerivatives();
-// for(unsigned j=0;j<mycolv->atomsWithCatomDer.getNumberActive();++j){
-// unsigned n=mycolv->atomsWithCatomDer[j], nx=3*n; atomsWithCatomDer.activate(n);
-// addElementDerivative(nbase + nx + 0, mycolv->getElementDerivative(nbas2 + nx + 0) );
-// addElementDerivative(nbase + nx + 1, mycolv->getElementDerivative(nbas2 + nx + 1) );
-// addElementDerivative(nbase + nx + 2, mycolv->getElementDerivative(nbas2 + nx + 2) );
-// }
-// }
-// atomsWithCatomDer.updateActiveMembers(); // This can perhaps be faster
-// return cvec;
-// }
-// Vector cvec;
-// for(unsigned i=0;i<3;++i) cvec[i]=getElementValue(1+i);
-// return cvec;
-// }
-
void BridgedMultiColvarFunction::calculateNumericalDerivatives( ActionWithValue* a ){
if(!a){
a=dynamic_cast<ActionWithValue*>(this);
diff --git a/src/vesselbase/ActionWithVessel.cpp b/src/vesselbase/ActionWithVessel.cpp
index 475298519..9f1639406 100644
--- a/src/vesselbase/ActionWithVessel.cpp
+++ b/src/vesselbase/ActionWithVessel.cpp
@@ -56,6 +56,7 @@ ActionWithVessel::ActionWithVessel(const ActionOptions&ao):
lowmem(false),
noderiv(true),
actionIsBridged(false),
+ mydata(NULL),
contributorsAreUnlocked(false),
weightHasDerivatives(false)
{
@@ -104,6 +105,10 @@ void ActionWithVessel::addVessel( Vessel* vv ){
ShortcutVessel* sv=dynamic_cast<ShortcutVessel*>(vv);
if(!sv){ vv->checkRead(); functions.push_back(vv); }
else { delete sv; }
+
+ StoreDataVessel* mm=dynamic_cast<StoreDataVessel*>( vv );
+ if( mydata && mm ) error("cannot have more than one StoreDataVessel in one action");
+ else mydata=mm;
}
BridgeVessel* ActionWithVessel::addBridgingVessel( ActionWithVessel* tome ){
@@ -117,15 +122,12 @@ BridgeVessel* ActionWithVessel::addBridgingVessel( ActionWithVessel* tome ){
}
StoreDataVessel* ActionWithVessel::buildDataStashes( const bool& allow_wcutoff, const double& wtol ){
- for(unsigned i=0;i<functions.size();++i){
- StoreDataVessel* vsv=dynamic_cast<StoreDataVessel*>( functions[i] );
- if( vsv ) return vsv;
- }
+ if(mydata) return mydata;
VesselOptions da("","",0,"",this);
- StoreDataVessel* mydata=new StoreDataVessel(da);
- if( allow_wcutoff ) mydata->setHardCutoffOnWeight( wtol );
- addVessel(mydata);
+ StoreDataVessel* mm=new StoreDataVessel(da);
+ if( allow_wcutoff ) mm->setHardCutoffOnWeight( wtol );
+ addVessel(mm);
// Make sure resizing of vessels is done
resizeFunctions();
@@ -278,6 +280,9 @@ void ActionWithVessel::runAllTasks(){
// Get size for buffer
unsigned bsize=0, bufsize=getSizeOfBuffer( bsize );
+ std::vector<unsigned> der_list;
+ if( mydata ) der_list.resize( mydata->getSizeOfDerivativeList(), 0 );
+
// Build storage stuff for loop
std::vector<double> buffer( bufsize, 0.0 );
MultiValue myvals( getNumberOfQuantities(), getNumberOfDerivatives() );
@@ -304,11 +309,17 @@ void ActionWithVessel::runAllTasks(){
// Now calculate all the functions
// If the contribution of this quantity is very small at neighbour list time ignore it
// untill next neighbour list time
- if( !calculateAllVessels( indexOfTaskInFullList[i], myvals, bvals, buffer ) && contributorsAreUnlocked ) deactivate_task( indexOfTaskInFullList[i] );
+ if( !calculateAllVessels( indexOfTaskInFullList[i], myvals, bvals, buffer, der_list ) && contributorsAreUnlocked ) deactivate_task( indexOfTaskInFullList[i] );
+
+ // Clear the value
myvals.clearAll();
}
// MPI Gather everything
if( !serial && buffer.size()>0 ) comm.Sum( buffer );
+ // MPI Gather index stores
+ if( mydata && !lowmem && !noderiv ){
+ comm.Sum( der_list ); mydata->setActiveValsAndDerivatives( der_list );
+ }
// Update the elements that are makign contributions to the sum here
// this causes problems if we do it in prepare
if( !serial && contributorsAreUnlocked ) comm.Sum( taskFlags );
@@ -320,20 +331,12 @@ void ActionWithVessel::transformBridgedDerivatives( const unsigned& current, Mul
plumed_error();
}
-// void ActionWithVessel::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ){
-// indices[jstore]=getNumberOfDerivatives();
-// if( indices[jstore]>maxder ) error("too many derivatives to store. Run with LOWMEM");
-//
-// unsigned kder = ntotal + jstore*getNumberOfDerivatives();
-// for(unsigned jder=0;jder<getNumberOfDerivatives();++jder){ indices[ kder ] = jder; kder++; }
-// }
-
-bool ActionWithVessel::calculateAllVessels( const unsigned& taskCode, MultiValue& myvals, MultiValue& bvals, std::vector<double>& buffer ){
+bool ActionWithVessel::calculateAllVessels( const unsigned& taskCode, MultiValue& myvals, MultiValue& bvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ){
bool keep=false;
for(unsigned j=0;j<functions.size();++j){
// Calculate returns a bool that tells us if this particular
// quantity is contributing more than the tolerance
- if( functions[j]->calculate( taskCode, functions[j]->transformDerivatives(taskCode, myvals, bvals), buffer ) ) keep=true;
+ if( functions[j]->calculate( taskCode, functions[j]->transformDerivatives(taskCode, myvals, bvals), buffer, der_list ) ) keep=true;
if( !actionIsBridged ) bvals.clearAll();
}
return keep;
diff --git a/src/vesselbase/ActionWithVessel.h b/src/vesselbase/ActionWithVessel.h
index e57a93ce1..f8ea4c798 100644
--- a/src/vesselbase/ActionWithVessel.h
+++ b/src/vesselbase/ActionWithVessel.h
@@ -68,6 +68,8 @@ private:
double nl_tolerance;
/// Pointers to the functions we are using on each value
std::vector<Vessel*> functions;
+/// A pointer to the object that stores data
+ StoreDataVessel* mydata;
/// Tempory storage for forces
std::vector<double> tmpforces;
/// Ths full list of tasks we have to perform
@@ -110,7 +112,7 @@ protected:
void resizeFunctions();
/// This loops over all the vessels calculating them and also
/// sets all the element derivatives equal to zero
- bool calculateAllVessels( const unsigned& taskCode, MultiValue& myvals, MultiValue& bvals, std::vector<double>& buffer );
+ bool calculateAllVessels( const unsigned& taskCode, MultiValue& myvals, MultiValue& bvals, std::vector<double>& buffer, std::vector<unsigned>& der_list );
/// Retrieve the forces from all the vessels (used in apply)
bool getForcesFromVessels( std::vector<double>& forcesToApply );
/// Is the calculation being done in serial
diff --git a/src/vesselbase/Between.cpp b/src/vesselbase/Between.cpp
index 2a3dabea5..af2024b09 100644
--- a/src/vesselbase/Between.cpp
+++ b/src/vesselbase/Between.cpp
@@ -67,7 +67,7 @@ std::string Between::function_description(){
return "the number of values " + hist.description();
}
-double Between::calcTransform( const double& val, double& dv ){
+double Between::calcTransform( const double& val, double& dv ) const {
double f = hist.calculate(val, dv); return f;
}
diff --git a/src/vesselbase/Between.h b/src/vesselbase/Between.h
index 593f1993d..02f6eb059 100644
--- a/src/vesselbase/Between.h
+++ b/src/vesselbase/Between.h
@@ -36,7 +36,7 @@ public:
static void reserveKeyword( Keywords& keys );
Between( const VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
double getCutoff();
};
diff --git a/src/vesselbase/BridgeVessel.cpp b/src/vesselbase/BridgeVessel.cpp
index dceec7704..41cb4eb84 100644
--- a/src/vesselbase/BridgeVessel.cpp
+++ b/src/vesselbase/BridgeVessel.cpp
@@ -28,8 +28,8 @@ namespace vesselbase {
BridgeVessel::BridgeVessel( const VesselOptions& da ):
Vessel(da),
-inum(0),
-in_normal_calculate(false)
+inum(0)
+// in_normal_calculate(false)
{
}
@@ -71,13 +71,13 @@ MultiValue& BridgeVessel::transformDerivatives( const unsigned& current, MultiVa
return outvals;
}
-bool BridgeVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer ){
- in_normal_calculate=true;
+bool BridgeVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
+ // in_normal_calculate=true;
if( myvals.get(0)<myOutputAction->getTolerance() ){
return ( !myOutputAction->contributorsAreUnlocked || myvals.get(0)>=myOutputAction->getNLTolerance() );
}
- bool keep=myOutputAction->calculateAllVessels( current, myvals, myvals, buffer );
- in_normal_calculate=false;
+ bool keep=myOutputAction->calculateAllVessels( current, myvals, myvals, buffer, der_list );
+ // in_normal_calculate=false;
return ( !myOutputAction->contributorsAreUnlocked || keep );
}
diff --git a/src/vesselbase/BridgeVessel.h b/src/vesselbase/BridgeVessel.h
index fc6c914bd..fedaf39ea 100644
--- a/src/vesselbase/BridgeVessel.h
+++ b/src/vesselbase/BridgeVessel.h
@@ -40,7 +40,7 @@ it is created in a different Action however. At the moment this is used for reg
class BridgeVessel : public Vessel {
private:
unsigned inum;
- bool in_normal_calculate;
+ // bool in_normal_calculate;
std::vector<double> mynumerical_values;
ActionWithVessel* myOutputAction;
ActionWithValue* myOutputValues;
@@ -63,20 +63,13 @@ public:
/// This transforms the derivatives using the output value
MultiValue& transformDerivatives( const unsigned& current, MultiValue& invals, MultiValue& outvals );
/// Actually do the calculation
- bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer );
+ bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_index ) const ;
/// Finish the calculation
void finish( const std::vector<double>& buffer );
/// Calculate numerical derivatives
void completeNumericalDerivatives();
-/// This is used to tell if the bridge has been called in recompute
- bool prerequisitsCalculated();
};
-inline
-bool BridgeVessel::prerequisitsCalculated(){
- return in_normal_calculate;
-}
-
}
}
#endif
diff --git a/src/vesselbase/FunctionVessel.cpp b/src/vesselbase/FunctionVessel.cpp
index 5aad279d7..02e7a6d69 100644
--- a/src/vesselbase/FunctionVessel.cpp
+++ b/src/vesselbase/FunctionVessel.cpp
@@ -73,7 +73,7 @@ void FunctionVessel::setNumberOfDerivatives( const unsigned& nder ){
final_value->resizeDerivatives( nder );
}
-bool FunctionVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer ){
+bool FunctionVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
double weight=myvals.get(0);
plumed_dbg_assert( weight>=getTolerance() );
@@ -96,7 +96,7 @@ bool FunctionVessel::calculate( const unsigned& current, MultiValue& myvals, std
return true;
}
-double FunctionVessel::calcTransform( const double& , double& ){
+double FunctionVessel::calcTransform( const double& , double& ) const {
plumed_error(); return 1.0;
}
diff --git a/src/vesselbase/FunctionVessel.h b/src/vesselbase/FunctionVessel.h
index 08157928f..9c787c96a 100644
--- a/src/vesselbase/FunctionVessel.h
+++ b/src/vesselbase/FunctionVessel.h
@@ -53,8 +53,6 @@ protected:
bool usetol;
/// Set the final value
void setOutputValue( const double& val );
-/// This does a combination of the product and chain rules
- void mergeFinalDerivatives( const std::vector<double>& df );
/// Resize the vector containing the derivatives
void setNumberOfDerivatives( const unsigned& nder );
/// Return a pointer to the final value
@@ -71,9 +69,9 @@ public:
/// The rest of the description of what we are calculating
virtual std::string function_description()=0;
/// Do the calcualtion
- virtual bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer );
+ virtual bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const ;
/// Do any transformations of the value that are required
- virtual double calcTransform( const double& val, double& df );
+ virtual double calcTransform( const double& val, double& df ) const ;
/// Finish the calculation of the quantity
virtual void finish( const std::vector<double>& buffer );
/// Finish with any transforms required
diff --git a/src/vesselbase/LessThan.cpp b/src/vesselbase/LessThan.cpp
index 479f3afac..2c3b98ce4 100644
--- a/src/vesselbase/LessThan.cpp
+++ b/src/vesselbase/LessThan.cpp
@@ -54,7 +54,7 @@ std::string LessThan::function_description(){
return "the number of values less than " + sf.description();
}
-double LessThan::calcTransform( const double& val, double& dv ){
+double LessThan::calcTransform( const double& val, double& dv ) const {
double f = sf.calculate(val, dv); dv*=val; return f;
}
diff --git a/src/vesselbase/LessThan.h b/src/vesselbase/LessThan.h
index 24bf15148..7570618ec 100644
--- a/src/vesselbase/LessThan.h
+++ b/src/vesselbase/LessThan.h
@@ -37,7 +37,7 @@ public:
static void reserveKeyword( Keywords& keys );
LessThan( const VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
double getCutoff();
};
diff --git a/src/vesselbase/Max.cpp b/src/vesselbase/Max.cpp
index 13b5a995c..e27dabd79 100644
--- a/src/vesselbase/Max.cpp
+++ b/src/vesselbase/Max.cpp
@@ -34,7 +34,7 @@ public:
static void reserveKeyword( Keywords& keys );
Max( const VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
double finalTransform( const double& val, double& dv );
};
@@ -69,7 +69,7 @@ std::string Max::function_description(){
return "the maximum value. Beta is equal to " + str_beta;
}
-double Max::calcTransform( const double& val, double& dv ){
+double Max::calcTransform( const double& val, double& dv ) const {
double f = exp(val/beta); dv=f/beta; return f;
}
diff --git a/src/vesselbase/Mean.cpp b/src/vesselbase/Mean.cpp
index 529788360..764629e7c 100644
--- a/src/vesselbase/Mean.cpp
+++ b/src/vesselbase/Mean.cpp
@@ -32,7 +32,7 @@ public:
static void reserveKeyword( Keywords& keys );
Mean( const vesselbase::VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
};
PLUMED_REGISTER_VESSEL(Mean,"MEAN")
@@ -58,7 +58,7 @@ std::string Mean::function_description(){
return "the mean value";
}
-double Mean::calcTransform( const double& val, double& dv ){
+double Mean::calcTransform( const double& val, double& dv ) const {
dv=1.0; return val;
}
diff --git a/src/vesselbase/Min.cpp b/src/vesselbase/Min.cpp
index a14c1f6bb..8e5ba1a42 100644
--- a/src/vesselbase/Min.cpp
+++ b/src/vesselbase/Min.cpp
@@ -34,7 +34,7 @@ public:
static void reserveKeyword( Keywords& keys );
Min( const VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
double finalTransform( const double& val, double& dv );
};
@@ -68,7 +68,7 @@ std::string Min::function_description(){
return "the minimum value. Beta is equal to " + str_beta;
}
-double Min::calcTransform( const double& val, double& dv ){
+double Min::calcTransform( const double& val, double& dv ) const {
double f = exp(beta/val); dv=f/(val*val);
return f;
}
diff --git a/src/vesselbase/MoreThan.cpp b/src/vesselbase/MoreThan.cpp
index 801248155..938da5d6b 100644
--- a/src/vesselbase/MoreThan.cpp
+++ b/src/vesselbase/MoreThan.cpp
@@ -36,7 +36,7 @@ public:
static void reserveKeyword( Keywords& keys );
MoreThan( const VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
};
PLUMED_REGISTER_VESSEL(MoreThan,"MORE_THAN")
@@ -68,7 +68,7 @@ std::string MoreThan::function_description(){
return "the number of values more than " + sf.description();
}
-double MoreThan::calcTransform( const double& val, double& dv ){
+double MoreThan::calcTransform( const double& val, double& dv ) const {
double f = 1.0 - sf.calculate(val, dv); dv*=-val; return f;
}
diff --git a/src/vesselbase/ShortcutVessel.h b/src/vesselbase/ShortcutVessel.h
index b1a2d88f2..0e58d50c5 100644
--- a/src/vesselbase/ShortcutVessel.h
+++ b/src/vesselbase/ShortcutVessel.h
@@ -39,7 +39,7 @@ public:
ShortcutVessel( const VesselOptions& );
std::string description(){ return ""; }
void resize(){ plumed_error(); }
- bool calculate( const unsigned& taskCode, MultiValue& myvals, std::vector<double>& buffer ){ plumed_error(); }
+ bool calculate( const unsigned& taskCode, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_index ) const { plumed_error(); }
void finish( const std::vector<double>& buffer ){ plumed_error(); }
bool applyForce( std::vector<double>& forces ){ plumed_error(); }
};
diff --git a/src/vesselbase/StoreDataVessel.cpp b/src/vesselbase/StoreDataVessel.cpp
index b1b35f484..b496ce841 100644
--- a/src/vesselbase/StoreDataVessel.cpp
+++ b/src/vesselbase/StoreDataVessel.cpp
@@ -49,80 +49,46 @@ bool StoreDataVessel::weightCutoffIsOn() const {
return hard_cut;
}
-// void StoreDataVessel::completeSetup( const unsigned& dstart, const unsigned& nvec ){
-// if( (dstart+nvec)>getAction()->getNumberOfQuantities() ) error("this vessel can not be used with this action");
-// data_start=dstart; vecsize = nvec; // fvec.resize( vecsize );
-// }
-
void StoreDataVessel::resize(){
plumed_dbg_assert( vecsize>0 );
-// if( getAction()->derivativesAreRequired() ) final_derivatives.resize( getAction()->getNumberOfDerivatives() );
if( getAction()->lowmem || !getAction()->derivativesAreRequired() ){
nspace = 1;
active_der.resize( max_lowmem_stash * ( 1 + getAction()->getNumberOfDerivatives() ) );
-// local_derivatives.resize( max_lowmem_stash * vecsize * getAction()->getNumberOfDerivatives() );
} else {
nspace = 1 + getAction()->maxderivatives;
active_der.resize( getAction()->getFullNumberOfTasks() * ( 1 + getAction()->maxderivatives ) );
}
- active_val.resize( getAction()->getFullNumberOfTasks() );
+ //active_val.resize( getAction()->getFullNumberOfTasks() );
resizeBuffer( getAction()->getFullNumberOfTasks()*vecsize*nspace );
local_buffer.resize( getAction()->getFullNumberOfTasks()*vecsize*nspace );
}
-void StoreDataVessel::prepare(){
-// Clear bookeeping arrays
- active_der.assign(active_der.size(),0);
- active_val.assign(active_val.size(),0);
-}
-
-// void StoreDataVessel::getIndexList( const unsigned& ntotal, const unsigned& jstore, const unsigned& maxder, std::vector<unsigned>& indices ){
-// // getAction()->getIndexList( ntotal, jstore, maxder, indices );
-// }
-//
-// void StoreDataVessel::setTaskToRecompute( const unsigned& ivec ){
-// // getAction()->current = getAction()->fullTaskList[ivec];
-// // getAction()->task_index = ivec;
-// }
-//
-// void StoreDataVessel::recompute( const unsigned& ivec, const unsigned& jstore ){
-// plumed_dbg_assert( getAction()->derivativesAreRequired() && getAction()->lowmem && jstore<max_lowmem_stash );
-// // Set the task we want to reperform
-// setTaskToRecompute( ivec );
-// // Reperform the task
-// performTask( jstore );
-// // Store the derivatives
-// storeDerivativesLowMem( jstore );
-//
-// // Clear up afterwards
-// // getAction()->clearAfterTask();
+// void StoreDataVessel::prepare(){
+// // Clear bookeeping arrays
+// // active_der.assign(active_der.size(),0);
+// //active_val.assign(active_val.size(),0);
// }
-void StoreDataVessel::storeValues( const unsigned& myelem, MultiValue& myvals, std::vector<double>& buffer ){
- unsigned ibuf = bufstart + myelem * vecsize * nspace; active_val[myelem]=1;
+void StoreDataVessel::storeValues( const unsigned& myelem, MultiValue& myvals, std::vector<double>& buffer ) const {
+ unsigned ibuf = bufstart + myelem * vecsize * nspace; // active_val[myelem]=1;
for(unsigned icomp=0;icomp<vecsize;++icomp){
buffer[ibuf] = myvals.get(icomp); ibuf+=nspace;
}
}
-void StoreDataVessel::storeDerivatives( const unsigned& myelem, MultiValue& myvals, std::vector<double>& buffer ){
+void StoreDataVessel::storeDerivatives( const unsigned& myelem, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
plumed_dbg_assert( getAction()->derivativesAreRequired() && myelem<getAction()->getFullNumberOfTasks() );
- active_der[myelem]=myvals.getNumberActive();
- // getIndexList( act->getFullNumberOfTasks(), myelem, nspace-1, active_der );
+ der_list[myelem]=myvals.getNumberActive();
// Store the values of the components and the derivatives if
- // unsigned nder =getAction()->getNumberOfDerivatives();
for(unsigned icomp=0;icomp<vecsize;++icomp){
unsigned ibuf = bufstart + myelem * ( vecsize*nspace ) + icomp*nspace + 1;
unsigned kder = getAction()->getFullNumberOfTasks() + myelem * ( nspace - 1 );
for(unsigned j=0;j<myvals.getNumberActive();++j){
unsigned jder=myvals.getActiveIndex(j);
buffer[ibuf] = myvals.getDerivative( icomp, jder );
- active_der[kder] = jder;
- // act->getElementDerivative(nder*icomp + active_der[ kder ]);
- //addToBufferElement( ibuf, act->getElementDerivative(nder*icomp + active_der[ kder ]) );
- ibuf++; kder++;
+ der_list[kder] = jder; ibuf++; kder++;
}
}
}
@@ -199,130 +165,51 @@ void StoreDataVessel::retrieveDerivatives( const unsigned& myelem, const bool& n
}
}
+bool StoreDataVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
-//
-// void StoreDataVessel::storeDerivativesLowMem( const unsigned& jstore ){
-// plumed_dbg_assert( getAction()->derivativesAreRequired() );
-// // Store the indexes that have derivatives
-// ActionWithVessel* act=getAction();
-// unsigned nder = act->getNumberOfDerivatives();
-// getIndexList( max_lowmem_stash, jstore, nder, active_der );
-//
-// // Stash the derivatives
-// for(unsigned icomp=data_start;icomp<data_start + vecsize;++icomp){
-// unsigned ibuf = jstore * vecsize * nder + (icomp-data_start)*nder;
-// unsigned kder = max_lowmem_stash + jstore*nder;
-// for(unsigned jder=0;jder<active_der[jstore];++jder){
-// // local_derivatives[ibuf] = act->getElementDerivative( nder*icomp + active_der[ kder ] );
-// ibuf++; kder++;
-// }
-// }
-// }
-
-bool StoreDataVessel::calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer ){
-
- if( !hard_cut ){
- storeValues( current, myvals, buffer );
- if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ) storeDerivatives( current, myvals, buffer );
- } else if( myvals.get(0)>wtol ){
- storeValues( current, myvals, buffer );
- if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ) storeDerivatives( current, myvals, buffer );
- }
-
-// unsigned myelem = getAction()->getCurrentPositionInTaskList();
- // Normalize vector if it is required
-// unsigned myelem; finishTask( myelem );
+ if( !hard_cut ){
+ storeValues( current, myvals, buffer );
+ if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ) storeDerivatives( current, myvals, buffer, der_list );
+ } else if( myvals.get(0)>wtol ){
+ storeValues( current, myvals, buffer );
+ if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ) storeDerivatives( current, myvals, buffer, der_list );
+ }
- // Store the values
-// if( !hard_cut ){
-// storeValues( myelem, buffer );
-// // Store the derivatives if we are not using low memory
-// if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ) storeDerivativesHighMem( myelem, buffer );
-// } else if( getAction()->getElementValue(0)>wtol ){
-// storeValues( myelem, buffer );
-// // Store the derivatives if we are not using low memory
-// if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ) storeDerivativesHighMem( myelem, buffer );
-// }
-//
return true;
}
+// void StoreDataVessel::buildIndexStores( const unsigned& current, MultiValue& myvals, std::vector<unsigned>& val_index, std::vector<unsigned>& der_index ) const {
+// if( !hard_cut ){
+// val_index[current]=1;
+// if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ){
+// der_index[current]=myvals.getNumberActive();
+// unsigned kder = getAction()->getFullNumberOfTasks() + current * ( nspace - 1 );
+// for(unsigned j=0;j<myvals.getNumberActive();++j){ der_index[kder] = myvals.getActiveIndex(j); kder++; }
+// }
+// } else if( myvals.get(0)>wtol ){
+// val_index[current]=1;
+// if( !(getAction()->lowmem) && getAction()->derivativesAreRequired() ){
+// der_index[current]=myvals.getNumberActive();
+// unsigned kder = getAction()->getFullNumberOfTasks() + current * ( nspace - 1 );
+// for(unsigned j=0;j<myvals.getNumberActive();++j){ der_index[kder] = myvals.getActiveIndex(j); kder++; }
+// }
+// }
+// }
+
void StoreDataVessel::finish( const std::vector<double>& buffer ){
// Store the buffer locally
for(unsigned i=0;i<local_buffer.size();++i) local_buffer[i]=buffer[bufstart+i];
-
- // Update what variables we need
- comm.Sum( &active_val[0], active_val.size() );
-
- // Get the active derivatives
- if(!getAction()->lowmem && getAction()->derivativesAreRequired() ) comm.Sum( &active_der[0], active_der.size() );
}
-// double StoreDataVessel::chainRule( const unsigned& ival, const unsigned& ider, const std::vector<double>& df ){
-// plumed_dbg_assert( getAction()->derivativesAreRequired() && df.size()==vecsize );
-// // Clear final derivatives array
-// final_derivatives.assign( final_derivatives.size(), 0.0 );
-//
-// double dfout = 0.0;
-// if(getAction()->lowmem){
-// plumed_dbg_assert( ival<max_lowmem_stash );
-// unsigned maxder = getAction()->getNumberOfDerivatives();
-// unsigned ibuf=ival*(vecsize*maxder) + ider;
-// for(unsigned icomp=0;icomp<vecsize;++icomp){
-// dfout+=df[icomp]*local_derivatives[ibuf];
-// ibuf+=maxder;
-// }
-// } else {
-// plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() );
-// unsigned ibuf=ival*(vecsize*nspace) + 1 + ider;
-// for(unsigned icomp=0;icomp<vecsize;++icomp){
-// dfout+=df[icomp]*local_buffer[ibuf]; //getBufferElement(ibuf);
-// ibuf+=nspace;
-// }
-// }
-// return dfout;
-// }
-// void StoreDataVessel::chainRule( const unsigned& ival, const std::vector<double>& df ){
-// plumed_dbg_assert( getAction()->derivativesAreRequired() && df.size()==vecsize );
-// // Clear final derivatives array
-// final_derivatives.assign( final_derivatives.size(), 0.0 );
-//
-// if(getAction()->lowmem){
-// plumed_dbg_assert( ival<max_lowmem_stash );
-// unsigned maxder = getAction()->getNumberOfDerivatives();
-// for(unsigned ider=0;ider<active_der[ival];++ider){
-// final_derivatives[ider]=0.0;
-// unsigned ibuf=ival*(vecsize*maxder) + ider;
-// for(unsigned jcomp=0;jcomp<vecsize;++jcomp){
-// final_derivatives[ider]+=df[jcomp]*local_derivatives[ibuf];
-// ibuf+=maxder;
-// }
-// }
-// } else {
-// plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() );
-// for(unsigned ider=0;ider<active_der[ival];++ider){
-// final_derivatives[ider]=0.0;
-// unsigned ibuf=ival*(vecsize*nspace) + 1 + ider;
-// for(unsigned jcomp=0;jcomp<vecsize;++jcomp){
-// final_derivatives[ider]+=df[jcomp]*local_buffer[ibuf];
-// //final_derivatives[ider]+=df[jcomp]*getBufferElement(ibuf);
-// ibuf+=nspace;
-// }
-// }
+void StoreDataVessel::setActiveValsAndDerivatives( const std::vector<unsigned>& der_index ){
+// for(unsigned i=0;i<val_index.size();++i){ // Need to think about this bit GAT
+// if( ) active_val[i] // =val_index[i];
// }
-// }
-
-// void StoreDataVessel::chainRule( const unsigned& ival, const std::vector<double>& df, Value* val ){
-// plumed_dbg_assert( getAction()->derivativesAreRequired() && val->getNumberOfDerivatives()==final_derivatives.size() );
-// chainRule( ival, df );
-//
-// unsigned kder;
-// if( getAction()->lowmem ) kder = max_lowmem_stash + ival*getAction()->getNumberOfDerivatives();
-// else kder = getAction()->getFullNumberOfTasks() + ival*(nspace-1);
-//
-// for(unsigned i=0;i<active_der[ival];++i) val->addDerivative( active_der[kder+i] , final_derivatives[i] );
-// }
+ if( !getAction()->lowmem && getAction()->derivativesAreRequired() ){
+ for(unsigned i=0;i<der_index.size();++i) active_der[i]=der_index[i];
+ }
+}
}
}
diff --git a/src/vesselbase/StoreDataVessel.h b/src/vesselbase/StoreDataVessel.h
index 02a0f7f93..77b537cc5 100644
--- a/src/vesselbase/StoreDataVessel.h
+++ b/src/vesselbase/StoreDataVessel.h
@@ -51,17 +51,11 @@ private:
/// The amount of data per vector element
unsigned nspace;
/// The currently active values
- std::vector<unsigned> active_val;
+// std::vector<unsigned> active_val;
/// The active derivative elements
std::vector<unsigned> active_der;
-/// This is a tempory vector that is used to store data
-// std::vector<double> fvec;
/// The buffer
std::vector<double> local_buffer;
-// /// The local derivatives
-// std::vector<double> local_derivatives;
-// /// The final derivatives
-// std::vector<double> final_derivatives;
protected:
/// Apply a hard cutoff on the weight
bool hard_cut;
@@ -77,15 +71,9 @@ protected:
/// Return value of nspace
unsigned getNumberOfDerivativeSpacesPerComponent() const ;
/// Retrieve the values from the underlying ActionWithVessel
- void storeValues( const unsigned& , MultiValue& , std::vector<double>& );
-/// Set the Task that needs redoing
-// void setTaskToRecompute( const unsigned& ivec );
-/// Set a component of one of the vectors
-// void setComponent( const unsigned& , const unsigned& , const double& );
-/// This is the proper chain rule for vectors
-// double chainRule( const unsigned&, const unsigned&, const std::vector<double>& );
-// /// Chain rule the vector and output derivatives to a value
-// void chainRule( const unsigned& , const std::vector<double>&, Value* );
+ void storeValues( const unsigned& , MultiValue& , std::vector<double>& ) const ;
+/// This stores the data we get from the calculation
+ void storeDerivatives( const unsigned& , MultiValue& myvals, std::vector<double>&, std::vector<unsigned>& ) const ;
/// Get the ibuf'th local derivative value
double getLocalDerivative( const unsigned& ibuf );
/// Set the ibuf'th local derivative value
@@ -106,40 +94,25 @@ public:
/// Do all resizing of data
virtual void resize();
/// Clear certain data before start of main loop
- virtual void prepare();
+// virtual void prepare();
///
virtual std::string description(){ return ""; }
/// Get the number of derivatives for the ith value
unsigned getNumberOfDerivatives( const unsigned& );
-/// Get one of the stored indexes
-// unsigned getStoredIndex( const unsigned& , const unsigned& );
-/// Get a component of the stored vector
-// double getComponent( const unsigned& , const unsigned& );
-/// Recalculate a vector - used in lowmem mode
-// virtual void recompute( const unsigned& , const unsigned& );
-/// This reperforms the task in the underlying action
-// virtual void performTask( const unsigned& );
-/// This reperforms the task
-// virtual void finishTask( const unsigned& ){};
-/// Chain rule and store output in local array called final_derivatives
-/// with vectors this does chain rule for dot products
-// void chainRule( const unsigned& , const std::vector<double>& );
-/// Get the ider'th final derivative value
-// double getFinalDerivative( const unsigned& ider ) const ;
+/// Get the size of the derivative list
+ unsigned getSizeOfDerivativeList() const ;
/// This stores the data when not using lowmem
- bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer );
-/// This stores the data we get from the calculation
-// void storeDerivativesLowMem( const unsigned& );
-/// This stores the data we get from the calculation
- void storeDerivatives( const unsigned& , MultiValue& myvals, std::vector<double>& );
+ bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_index ) const ;
+/// Build index stores
+// void buildIndexStores( const unsigned& current, MultiValue& myvals, std::vector<unsigned>& val_index, std::vector<unsigned>& der_index ) const ;
/// Final step in gathering data
virtual void finish( const std::vector<double>& buffer );
/// Is a particular stored value active at the present time
bool storedValueIsActive( const unsigned& iatom );
+/// Set the active values
+ void setActiveValsAndDerivatives( const std::vector<unsigned>& der_index );
/// Activate indexes (this is used at end of chain rule)
virtual void activateIndices( ActionWithVessel* ){}
-/// Get the list of indices that we are storing data for
-// virtual void getIndexList( const unsigned& , const unsigned& , const unsigned& , std::vector<unsigned>& );
/// Forces on vectors should always be applied elsewhere
virtual bool applyForce(std::vector<double>&){ return false; }
};
@@ -154,68 +127,21 @@ bool StoreDataVessel::usingLowMem(){
return getAction()->lowmem;
}
-// inline
-// void StoreDataVessel::performTask( const unsigned& ivec ){
-// // if( usingLowMem() ) getAction()->performTask();
-// }
-
-// inline
-// double StoreDataVessel::getComponent( const unsigned& ival, const unsigned& jcomp ){
-// plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() && jcomp<vecsize );
-// return 0.0; // GAT Broken
-// // return getBufferElement( ival*(vecsize*nspace) + jcomp*nspace );
-// }
-//
-// inline
-// void StoreDataVessel::setComponent( const unsigned& ival, const unsigned& jcomp, const double& val ){
-// plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() && jcomp<vecsize );
-// // setBufferElement( ival*(vecsize*nspace) + jcomp*nspace, val );
-// }
-
inline
unsigned StoreDataVessel::getNumberOfDerivativeSpacesPerComponent() const {
return nspace;
}
-// inline
-// unsigned StoreDataVessel::getNumberOfDerivatives( const unsigned& ival ){
-// plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() );
-// return active_der[ival];
-// }
-
-// inline
-// unsigned StoreDataVessel::getStoredIndex( const unsigned& ival, const unsigned& jindex ){
-// plumed_dbg_assert( ival<getAction()->getFullNumberOfTasks() && jindex<active_der[ival] );
-//
-// unsigned kder;
-// if( getAction()->lowmem ) kder = max_lowmem_stash + ival*getAction()->getNumberOfDerivatives();
-// else kder = getAction()->getFullNumberOfTasks() + ival*(nspace-1);
-//
-// return active_der[kder + jindex];
-// }
-
-// inline
-// double StoreDataVessel::getLocalDerivative( const unsigned& ibuf ){
-// plumed_dbg_assert( getAction()->lowmem && ibuf<local_derivatives.size() );
-// return local_derivatives[ibuf];
-// }
-//
-// inline
-// double StoreDataVessel::getFinalDerivative( const unsigned& ider ) const {
-// plumed_dbg_assert( ider<final_derivatives.size() );
-// return final_derivatives[ider];
-// }
-//
-// inline
-// void StoreDataVessel::setLocalDerivative( const unsigned& ibuf, const double& val ){
-// plumed_dbg_assert( getAction()->lowmem && ibuf<local_derivatives.size() );
-// local_derivatives[ibuf]=val;
-// }
-
inline
bool StoreDataVessel::storedValueIsActive( const unsigned& iatom ){
- plumed_dbg_assert( iatom<active_val.size() );
- return (active_val[iatom]==1);
+ plumed_dbg_assert( iatom<getAction()->getFullNumberOfTasks() );
+ if( !hard_cut ) return true;
+ return local_buffer[iatom*vecsize*nspace]>wtol; // (active_val[iatom]==1);
+}
+
+inline
+unsigned StoreDataVessel::getSizeOfDerivativeList() const {
+ return active_der.size();
}
}
diff --git a/src/vesselbase/Sum.cpp b/src/vesselbase/Sum.cpp
index 08ce670be..485844765 100644
--- a/src/vesselbase/Sum.cpp
+++ b/src/vesselbase/Sum.cpp
@@ -31,7 +31,7 @@ public:
static void reserveKeyword( Keywords& keys );
Sum( const VesselOptions& da );
std::string function_description();
- double calcTransform( const double& val, double& dv );
+ double calcTransform( const double& val, double& dv ) const ;
};
PLUMED_REGISTER_VESSEL(Sum,"SUM")
@@ -54,7 +54,7 @@ std::string Sum::function_description(){
return "the sum of all the values";
}
-double Sum::calcTransform( const double& val, double& dv ){
+double Sum::calcTransform( const double& val, double& dv ) const {
dv=1.0; return val;
}
diff --git a/src/vesselbase/Vessel.h b/src/vesselbase/Vessel.h
index 8ff117e6a..304669dc9 100644
--- a/src/vesselbase/Vessel.h
+++ b/src/vesselbase/Vessel.h
@@ -113,7 +113,7 @@ protected:
/// This returns the whole input line (it is used for less_than/more_than/between)
std::string getAllInput();
/// Return a pointer to the action we are working in
- ActionWithVessel* getAction();
+ ActionWithVessel* getAction() const ;
/// Return the value of the tolerance
double getTolerance() const ;
/// Return the value of the neighbor list tolerance
@@ -146,7 +146,7 @@ public:
/// This is replaced in bridges so we can transform the derivatives
virtual MultiValue& transformDerivatives( const unsigned& current, MultiValue& myvals, MultiValue& bvals );
/// Calculate the part of the vessel that is done in the loop
- virtual bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer )=0;
+ virtual bool calculate( const unsigned& current, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const = 0;
/// Complete the calculation once the loop is finished
virtual void finish( const std::vector<double>& )=0;
/// Reset the size of the buffers
@@ -233,7 +233,7 @@ double Vessel::getNLTolerance() const {
}
inline
-ActionWithVessel* Vessel::getAction(){
+ActionWithVessel* Vessel::getAction() const {
return action;
}
--
GitLab