void SecondaryStructureRMSD::setSecondaryStructure( std::vector<Vector>& structure, double bondlength, double units ){
// If we are in natural units get conversion factor from nm into natural length units
if( plumed.getAtoms().usingNaturalUnits() ){
error("cannot use this collective variable when using natural units");
}
plumed_massert( !(align_strands && align_atom_1==0 && align_atom_2==0), "you must use setAtomsFromStrands with strands cutoff");
// Convert into correct units
for(unsigned i=0;i<structure.size();++i){
structure[i][0]*=units; structure[i][1]*=units; structure[i][2]*=units;
}
if( references.size()==0 ){
finishTaskListUpdate();
readVesselKeywords();
if( getNumberOfVessels()==0 ){
double r0; parse("R_0",r0); double d0; parse("D_0",d0);
int nn; parse("NN",nn); int mm; parse("MM",mm);
std::ostringstream ostr;
ostr<<"RATIONAL R_0="<<r0<<" D_0="<<d0<<" NN="<<nn<<" MM="<<mm;
std::string input=ostr.str(); addVessel( "LESS_THAN", input, -1 ); // -1 here means that this value will be named getLabel()
readVesselKeywords(); // This makes sure resizing is done
}
}
// Set the reference structure
references.push_back( metricRegister().create<SingleDomainRMSD>( alignType ) );
unsigned nn=references.size()-1;
std::vector<double> align( structure.size(), 1.0 ), displace( structure.size(), 1.0 );
references[nn]->setBoundsOnDistances( true , bondlength ); // We always use pbc
references[nn]->setReferenceAtoms( structure, align, displace );
// references[nn]->setNumberOfAtoms( structure.size() );
}
ManyRestraintsBase::ManyRestraintsBase(const ActionOptions& ao):
Action(ao),
ActionWithValue(ao),
ActionPilot(ao),
ActionWithVessel(ao),
ActionWithInputVessel(ao)
{
// Read in the vessel we are action on
readArgument("bridge");
aves=dynamic_cast<ActionWithVessel*>( getDependencies()[0] );
plumed_assert( getDependencies().size()==1 && aves );
log.printf(" adding restraints on variables calculated by %s action with label %s\n",
aves->getName().c_str(),aves->getLabel().c_str());
// Add a task list in order to avoid problems
for(unsigned i=0; i<aves->getFullNumberOfTasks(); ++i) addTaskToList( aves->getTaskCode(i) );
// And turn on the derivatives (note problems here because of ActionWithValue)
turnOnDerivatives();
needsDerivatives();
// Now create the vessel
std::string fake_input="LABEL=bias";
addVessel( "SUM", fake_input, 0 );
readVesselKeywords();
}
MultiColvarFilter::MultiColvarFilter(const ActionOptions&ao):
Action(ao),
BridgedMultiColvarFunction(ao)
{
if( getPntrToMultiColvar()->isDensity() ) error("filtering density makes no sense");
readVesselKeywords();
}
void MultiColvarBase::setupMultiColvarBase(){
// Setup decoder array
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; }
}
// Resize stuff here
resizeLocalArrays();
// Setup underlying ActionWithVessel
readVesselKeywords();
}
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();
}
void MultiColvarBase::setupMultiColvarBase(){
// Setup decoder array
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; }
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 );
numberForCentralAtom = 1.0 / static_cast<double>( ablocks.size() );
}
// Setup underlying ActionWithVessel
readVesselKeywords();
}
void VectorMultiColvar::setVectorDimensionality( const unsigned& ncomp, const bool& comp, const int& nat ){
// Store number of derivatives and if vectors are complex
ncomponents = ncomp; complexvec=comp;
if(complexvec) dervec.resize( 2*ncomponents );
else dervec.resize( ncomponents );
// Read in the atoms if we are using multicolvar reading
int natoms=nat; readAtoms( natoms );
// Create the store vector object
std::string param; vesselbase::VesselOptions da("","",0,param,this);
Keywords keys; StoreVectorsVessel::registerKeywords( keys );
vesselbase::VesselOptions da2(da,keys);
vecs = new StoreVectorsVessel(da2);
// Add the vessel to the base
addVessel(vecs);
// Read in any vessels
readVesselKeywords();
// Resize a holder for the derivatives of the norm of the vector
}
ActionWithIntegral::ActionWithIntegral(const ActionOptions&ao):
Action(ao),
ActionWithInputGrid(ao)
{
plumed_assert( ingrid->getNumberOfComponents()==1 );
// Retrieve the volume of the grid (for integration)
volume = ingrid->getCellVolume();
// Create something that is going to calculate the sum of all the values
// at the various grid points - this is going to be the integral
std::string fake_input; addVessel( "SUM", fake_input, -1 ); readVesselKeywords();
// Now create task list - number of tasks is equal to the number of grid points
// as we have to evaluate the function at each grid points
for(unsigned i=0;i<ingrid->getNumberOfPoints();++i) addTaskToList(i);
// And activate all tasks
deactivateAllTasks();
for(unsigned i=0;i<ingrid->getNumberOfPoints();++i) taskFlags[i]=1;
lockContributors();
}
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();
}
