void StoreDataVessel::storeDerivatives( const unsigned& myelem, MultiValue& myvals, std::vector<double>& buffer, std::vector<unsigned>& der_list ) const {
plumed_dbg_assert( vecsize>0 && getAction()->derivativesAreRequired() && myelem<getAction()->getFullNumberOfTasks() );
unsigned jelem = getAction()->getPositionInCurrentTaskList( myelem );
if( getAction()->getFullNumberOfTasks()==getNumberOfStoredValues() ){
der_list[jelem]=myvals.getNumberActive();
unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );
for(unsigned j=0;j<myvals.getNumberActive();++j){ der_list[kder] = myvals.getActiveIndex(j); kder++; }
} else {
// This ensures that active indices are gathered correctly if
// we have multiple tasks contributing to a stored quantity
unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );
for(unsigned j=0;j<myvals.getNumberActive();++j){
bool found=false; unsigned jder = myvals.getActiveIndex(j);
for(unsigned k=0;k<der_list[jelem];++k){
if( der_list[kder+k]==jder ){ found=true; break; }
}
if(!found){ der_list[kder+der_list[jelem]]=jder; der_list[jelem]++; }
}
}
// Store the values of the components and the derivatives
for(unsigned icomp=0;icomp<vecsize;++icomp){
unsigned ibuf = bufstart + jelem * ( vecsize*nspace ) + icomp*nspace + 1;
for(unsigned j=0;j<myvals.getNumberActive();++j){
unsigned jder=myvals.getActiveIndex(j);
buffer[ibuf] += myvals.getDerivative( icomp, jder ); ibuf++;
}
}
}
void StoreDataVessel::retrieveDerivatives( const unsigned& myelem, const bool& normed, MultiValue& myvals ){
plumed_dbg_assert( myvals.getNumberOfValues()==vecsize && myvals.getNumberOfDerivatives()==getAction()->getNumberOfDerivatives() );
myvals.clearAll();
if( getAction()->lowmem ){
recalculateStoredQuantity( myelem, myvals );
if( normed ) getAction()->normalizeVectorDerivatives( myvals );
} else {
unsigned jelem = getAction()->getPositionInCurrentTaskList( myelem );
// Retrieve the derivatives for elements 0 and 1 - weight and norm
for(unsigned icomp=0;icomp<vecsize;++icomp){
unsigned ibuf = jelem * ( vecsize*nspace ) + icomp*nspace + 1;
unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );
for(unsigned j=0;j<active_der[jelem];++j){
myvals.addDerivative( icomp, active_der[kder], local_buffer[ibuf] );
kder++; ibuf++;
}
}
if( normed ) getAction()->normalizeVectorDerivatives( myvals );
// Now ensure appropriate parts of list are activated
myvals.emptyActiveMembers();
unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );
for(unsigned j=0;j<active_der[jelem];++j){ myvals.putIndexInActiveArray( active_der[kder] ); kder++; }
myvals.sortActiveList();
}
}
void StoreDataVessel::resize(){
vecsize=getAction()->getNumberOfQuantities();
plumed_dbg_assert( vecsize>0 );
if( getAction()->lowmem || !getAction()->derivativesAreRequired() ){
nspace = 1;
active_der.resize( max_lowmem_stash * ( 1 + getAction()->getNumberOfDerivatives() ) );
} else {
nspace = 1 + getAction()->maxderivatives;
active_der.resize( getNumberOfStoredValues() * ( 1 + getAction()->maxderivatives ) );
}
resizeBuffer( getNumberOfStoredValues()*vecsize*nspace );
local_buffer.resize( getNumberOfStoredValues()*vecsize*nspace );
}
void StoreDataVessel::storeValues( const unsigned& myelem, MultiValue& myvals, std::vector<double>& buffer ) const {
plumed_dbg_assert( vecsize>0 );
unsigned jelem = getAction()->getPositionInCurrentTaskList( myelem ); plumed_dbg_assert( jelem<getNumberOfStoredValues() );
unsigned ibuf = bufstart + jelem * vecsize * nspace;
for(unsigned icomp=0;icomp<vecsize;++icomp){
buffer[ibuf] += myvals.get(icomp); ibuf+=nspace;
}
}
void TrigonometricPathVessel::finish( const std::vector<double>& buffer ) {
// Store the data calculated during mpi loop
StoreDataVessel::finish( buffer );
// Get current value of all arguments
for(unsigned i=0; i<cargs.size(); ++i) cargs[i]=mymap->getArgument(i);
// Determine closest and second closest point to current position
double lambda=mymap->getLambda();
std::vector<double> dist( getNumberOfComponents() ), dist2( getNumberOfComponents() );;
retrieveSequentialValue( 0, false, dist );
retrieveSequentialValue( 1, false, dist2 );
iclose1=getStoreIndex(0); iclose2=getStoreIndex(1);
double mindist1=dist[0], mindist2=dist2[0];
if( lambda>0.0 ) {
mindist1=-std::log( dist[0] ) / lambda;
mindist2=-std::log( dist2[0] ) / lambda;
}
if( mindist2<mindist1 ) {
double tmp=mindist1; mindist1=mindist2; mindist2=tmp;
iclose1=getStoreIndex(1); iclose2=getStoreIndex(0);
}
for(unsigned i=2; i<getNumberOfStoredValues(); ++i) {
retrieveSequentialValue( i, false, dist );
double ndist=dist[0];
if( lambda>0.0 ) ndist=-std::log( dist[0] ) / lambda;
if( ndist<mindist1 ) {
mindist2=mindist1; iclose2=iclose1;
mindist1=ndist; iclose1=getStoreIndex(i);
} else if( ndist<mindist2 ) {
mindist2=ndist; iclose2=getStoreIndex(i);
}
}
// And find third closest point
int isign = iclose1 - iclose2;
if( isign>1 ) isign=1; else if( isign<-1 ) isign=-1;
int iclose3 = iclose1 + isign; double v2v2;
// We now have to compute vectors connecting the three closest points to the
// new point
double v1v1 = (mymap->getReferenceConfiguration( iclose1 ))->calculate( mymap->getPositions(), mymap->getPbc(), mymap->getArguments(), mypack1, true );
double v3v3 = (mymap->getReferenceConfiguration( iclose2 ))->calculate( mymap->getPositions(), mymap->getPbc(), mymap->getArguments(), mypack3, true );
if( iclose3<0 || iclose3>=mymap->getFullNumberOfTasks() ) {
ReferenceConfiguration* conf2=mymap->getReferenceConfiguration( iclose1 );
v2v2=(mymap->getReferenceConfiguration( iclose2 ))->calc( conf2->getReferencePositions(), mymap->getPbc(), mymap->getArguments(),
conf2->getReferenceArguments(), mypack2, true );
(mymap->getReferenceConfiguration( iclose2 ))->extractDisplacementVector( conf2->getReferencePositions(), mymap->getArguments(),
conf2->getReferenceArguments(), false, projdir );
} else {
ReferenceConfiguration* conf2=mymap->getReferenceConfiguration( iclose3 );
v2v2=(mymap->getReferenceConfiguration( iclose1 ))->calc( conf2->getReferencePositions(), mymap->getPbc(), mymap->getArguments(),
conf2->getReferenceArguments(), mypack2, true );
(mymap->getReferenceConfiguration( iclose1 ))->extractDisplacementVector( conf2->getReferencePositions(), mymap->getArguments(),
conf2->getReferenceArguments(), false, projdir );
}
// Stash derivatives of v1v1
for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) mypack1_stashd_args[i]=mypack1.getArgumentDerivative(i);
if( mymap->getNumberOfAtoms()>0 ) {
ReferenceAtoms* at = dynamic_cast<ReferenceAtoms*>( mymap->getReferenceConfiguration( iclose1 ) );
const std::vector<double> & displace( at->getDisplace() );
for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) {
mypack1_stashd_atoms[i]=mypack1.getAtomDerivative(i); mypack1.getAtomsDisplacementVector()[i] /= displace[i];
}
}
// Calculate the dot product of v1 with v2
double v1v2 = (mymap->getReferenceConfiguration(iclose1))->projectDisplacementOnVector( projdir, mymap->getArguments(), cargs, mypack1 );
// This computes s value
double spacing = mymap->getPropertyValue( iclose1, (mymap->property.begin())->first ) - mymap->getPropertyValue( iclose2, (mymap->property.begin())->first );
double root = sqrt( v1v2*v1v2 - v2v2 * ( v1v1 - v3v3) );
dx = 0.5 * ( (root + v1v2) / v2v2 - 1.);
double path_s = mymap->getPropertyValue(iclose1, (mymap->property.begin())->first ) + spacing * dx; sp->set( path_s );
double fact = 0.25*spacing / v2v2;
// Derivative of s wrt arguments
for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) {
sp->setDerivative( i, fact*( mypack2.getArgumentDerivative(i) + (v2v2 * (-mypack1_stashd_args[i] + mypack3.getArgumentDerivative(i))
+ v1v2*mypack2.getArgumentDerivative(i) )/root ) );
}
// Derivative of s wrt atoms
unsigned narg=mymap->getNumberOfArguments(); Tensor vir; vir.zero(); fact = 0.5*spacing / v2v2;
if( mymap->getNumberOfAtoms()>0 ) {
for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) {
Vector ader = fact*(( v1v2*mypack1.getAtomDerivative(i) + 0.5*v2v2*(-mypack1_stashd_atoms[i] + mypack3.getAtomDerivative(i) ) )/root + mypack1.getAtomDerivative(i) );
for(unsigned k=0; k<3; ++k) sp->setDerivative( narg+3*i+k, ader[k] );
vir-=Tensor( mymap->getPosition(i), ader );
}
// Set the virial
unsigned nbase=narg+3*mymap->getNumberOfAtoms();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) sp->setDerivative( nbase+3*i+j, vir(i,j) );
}
// Now compute z value
ReferenceConfiguration* conf2=mymap->getReferenceConfiguration( iclose1 );
double v4v4=(mymap->getReferenceConfiguration( iclose2 ))->calc( conf2->getReferencePositions(), mymap->getPbc(), mymap->getArguments(),
conf2->getReferenceArguments(), mypack2, true );
// Extract vector connecting frames
(mymap->getReferenceConfiguration( iclose2 ))->extractDisplacementVector( conf2->getReferencePositions(), mymap->getArguments(),
conf2->getReferenceArguments(), false, projdir );
// Calculate projection of vector on line connnecting frames
double proj = (mymap->getReferenceConfiguration(iclose1))->projectDisplacementOnVector( projdir, mymap->getArguments(), cargs, mypack1 );
double path_z = v1v1 + dx*dx*v4v4 - 2*dx*proj;
// Derivatives for z path
path_z = sqrt(path_z); zp->set( path_z ); vir.zero();
for(unsigned i=0; i<mymap->getNumberOfArguments(); ++i) zp->setDerivative( i, (mypack1_stashd_args[i] - 2*dx*mypack1.getArgumentDerivative(i))/(2.0*path_z) );
// Derivative wrt atoms
if( mymap->getNumberOfAtoms()>0 ) {
for(unsigned i=0; i<mymap->getNumberOfAtoms(); ++i) {
Vector dxder; for(unsigned k=0; k<3; ++k) dxder[k] = ( 2*v4v4*dx - 2*proj )*spacing*sp->getDerivative( narg + 3*i+k );
Vector ader = ( mypack1_stashd_atoms[i] - 2.*dx*mypack1.getAtomDerivative(i) + dxder )/ (2.0*path_z);
for(unsigned k=0; k<3; ++k) zp->setDerivative( narg+3*i+k, ader[k] );
vir-=Tensor( mymap->getPosition(i), ader );
}
// Set the virial
unsigned nbase=narg+3*mymap->getNumberOfAtoms();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) zp->setDerivative( nbase+3*i+j, vir(i,j) );
}
}
