void VolumeGradientBase::requestAtoms( const std::vector<AtomNumber>& atoms ) {
ActionAtomistic::requestAtoms(atoms); bridgeVariable=3*atoms.size();
std::map<std::string,bool> checklabs;
for(const auto & p : getDependencies() ) checklabs.insert(std::pair<std::string,bool>(p->getLabel(),false));
for(const auto & p : plumed.getActionSet() ) {
if( p->getLabel()==getPntrToMultiColvar()->getLabel() ) break;
if( checklabs.count(p->getLabel()) ) checklabs[p->getLabel()]=true;
}
for(const auto & p : checklabs ) {
if( !p.second ) error("the input for the virtual atoms used in the input for this action must appear in the input file before the input multicolvar");
}
addDependency( getPntrToMultiColvar() );
tmpforces.resize( 3*atoms.size()+9 );
}
void MultiColvarFilter::completeTask( const unsigned& curr, MultiValue& invals, MultiValue& outvals ) const {
invals.copyValues( outvals );
if( derivativesAreRequired() ) invals.copyDerivatives( outvals );
// Retrive the value of the multicolvar and apply filter
double val=invals.get(1), df, weight=applyFilter( val, df );
// Now propegate derivatives
if( !getPntrToMultiColvar()->weightHasDerivatives ){
outvals.setValue( 0, weight );
if( derivativesAreRequired() ){
for(unsigned i=0;i<invals.getNumberActive();++i){
unsigned jder=invals.getActiveIndex(i);
outvals.addDerivative( 0, jder, df*invals.getDerivative(1, jder ) );
}
}
} else {
double ww=outvals.get(0); outvals.setValue( 0, ww*weight );
if( derivativesAreRequired() ){
for(unsigned i=0;i<outvals.getNumberActive();++i){
unsigned ider=outvals.getActiveIndex(i);
outvals.setDerivative( 0, ider, weight*outvals.getDerivative(1,ider) + ww*df*outvals.getDerivative(0,ider) );
}
}
}
}
MultiColvarFilter::MultiColvarFilter(const ActionOptions&ao):
Action(ao),
BridgedMultiColvarFunction(ao)
{
if( getPntrToMultiColvar()->isDensity() ) error("filtering density makes no sense");
readVesselKeywords();
}
bool ActionVolume::inVolumeOfInterest( const unsigned& curr ) const {
Vector catom_pos=getPntrToMultiColvar()->getCentralAtomPos( curr );
Vector wdf; Tensor vir; std::vector<Vector> refders( getNumberOfAtoms() );
double weight=calculateNumberInside( catom_pos, wdf, vir, refders );
if( not_in ) weight = 1.0 - weight;
if( weight<getTolerance() ) return false;
return true;
}
void VolumeGradientBase::completeTask( const unsigned& curr, MultiValue& invals, MultiValue& outvals ) const {
if( getPntrToMultiColvar()->isDensity() ) {
outvals.setValue(0, 1.0); outvals.setValue(1, 1.0);
} else {
// Copy derivatives of the colvar and the value of the colvar
invals.copyValues( outvals );
if( derivativesAreRequired() ) invals.copyDerivatives( outvals );
}
calculateAllVolumes( curr, outvals );
}
void ActionVolume::calculateAllVolumes( const unsigned& curr, MultiValue& outvals ) const {
Vector catom_pos=getPntrToMultiColvar()->getCentralAtomPos( curr );
double weight; Vector wdf; Tensor vir; std::vector<Vector> refders( getNumberOfAtoms() );
weight=calculateNumberInside( catom_pos, wdf, vir, refders );
if( not_in ) {
weight = 1.0 - weight; wdf *= -1.; vir *=-1;
for(unsigned i=0; i<refders.size(); ++i) refders[i]*=-1;
}
setNumberInVolume( 0, curr, weight, wdf, vir, refders, outvals );
}
MultiColvarFilter::MultiColvarFilter(const ActionOptions&ao):
Action(ao),
BridgedMultiColvarFunction(ao)
{
if( getPntrToMultiColvar()->isDensity() ) error("filtering/transforming density makes no sense");
if( getName().find("MFILTER")!=std::string::npos ) filter=true;
else {
plumed_assert( getName().find("MTRANSFORM")!=std::string::npos );
filter=false;
}
readVesselKeywords();
}
ActionVolume::ActionVolume(const ActionOptions&ao):
Action(ao),
VolumeGradientBase(ao)
{
// Find number of quantities
if( getPntrToMultiColvar()->isDensity() ) nquantities=2; // Value + weight
else if( getPntrToMultiColvar()->getNumberOfQuantities()==2 ) nquantities=2; // Value + weight
else nquantities = 1 + getPntrToMultiColvar()->getNumberOfQuantities()-2 + 1; // Norm + vector + weight
// Output some nice information
std::string functype=getPntrToMultiColvar()->getName();
std::transform( functype.begin(), functype.end(), functype.begin(), tolower );
log.printf(" calculating %s inside region of insterest\n",functype.c_str() );
parseFlag("OUTSIDE",not_in); sigma=0.0;
if( keywords.exists("SIGMA") ) parse("SIGMA",sigma);
if( keywords.exists("KERNEL") ) parse("KERNEL",kerneltype);
if( getPntrToMultiColvar()->isDensity() ) {
std::string input;
addVessel( "SUM", input, -1 ); // -1 here means that this value will be named getLabel()
}
readVesselKeywords();
}
void VolumeGradientBase::setNumberInVolume( const unsigned& ivol, const unsigned& curr, const double& weight,
const Vector& wdf, const Tensor& virial, const std::vector<Vector>& refders,
MultiValue& outvals ) const {
MultiColvarBase* mcolv=getPntrToMultiColvar();
if( !mcolv->weightHasDerivatives ) {
outvals.setValue(ivol, weight );
if( derivativesAreRequired() ) {
CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
unsigned jatom=3*catom.getIndex(i);
outvals.addDerivative( ivol, jatom+0, catom.getDerivative(i,0,wdf) );
outvals.addDerivative( ivol, jatom+1, catom.getDerivative(i,1,wdf) );
outvals.addDerivative( ivol, jatom+2, catom.getDerivative(i,2,wdf) );
}
unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, virial(i,j) );
for(unsigned i=0; i<refders.size(); ++i) {
unsigned iatom=nmder+3*i;
outvals.addDerivative( ivol, iatom+0, refders[i][0] );
outvals.addDerivative( ivol, iatom+1, refders[i][1] );
outvals.addDerivative( ivol, iatom+2, refders[i][2] );
}
}
} else if(ivol==0) {
double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
if( derivativesAreRequired() ) {
plumed_merror("This needs testing");
CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
unsigned jatom=3*catom.getIndex(i);
outvals.addDerivative( ivol, jatom+0, weight*outvals.getDerivative(ivol,jatom+0) + ww*catom.getDerivative(i,0,wdf) );
outvals.addDerivative( ivol, jatom+1, weight*outvals.getDerivative(ivol,jatom+1) + ww*catom.getDerivative(i,1,wdf) );
outvals.addDerivative( ivol, jatom+2, weight*outvals.getDerivative(ivol,jatom+2) + ww*catom.getDerivative(i,2,wdf) );
}
unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );
for(unsigned i=0; i<refders.size(); ++i) {
unsigned iatom=nmder+3*i;
outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
}
}
} else {
double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);
if( derivativesAreRequired() ) {
plumed_merror("This needs testing");
CatomPack catom; mcolv->getCentralAtomPack( 0, curr, catom );
for(unsigned i=0; i<catom.getNumberOfAtomsWithDerivatives(); ++i) {
unsigned jatom=3*catom.getIndex(i);
outvals.addDerivative( ivol, jatom+0, ww*catom.getDerivative(i,0,wdf) );
outvals.addDerivative( ivol, jatom+1, ww*catom.getDerivative(i,1,wdf) );
outvals.addDerivative( ivol, jatom+2, ww*catom.getDerivative(i,2,wdf) );
}
unsigned nmder=getPntrToMultiColvar()->getNumberOfDerivatives();
for(unsigned i=0; i<3; ++i) for(unsigned j=0; j<3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );
for(unsigned i=0; i<refders.size(); ++i) {
unsigned iatom=nmder+3*i;
outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );
outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );
outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );
}
}
}
}
