void ActionAtomistic::makeWhole(){
for(unsigned j=0;j<positions.size()-1;++j){
const Vector & first (positions[j]);
Vector & second (positions[j+1]);
second=first+pbcDistance(first,second);
}
}
// calculator
void CoordinationBase::calculate()
{
double ncoord=0.;
Tensor virial;
vector<Vector> deriv(getNumberOfAtoms());
// deriv.resize(getPositions().size());
if(nl->getStride()>0 && invalidateList){
nl->update(getPositions());
}
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if(serial){
stride=1;
rank=0;
}else{
stride=comm.Get_size();
rank=comm.Get_rank();
}
for(unsigned int i=rank;i<nl->size();i+=stride) { // sum over close pairs
Vector distance;
unsigned i0=nl->getClosePair(i).first;
unsigned i1=nl->getClosePair(i).second;
if(getAbsoluteIndex(i0)==getAbsoluteIndex(i1)) continue;
if(pbc){
distance=pbcDistance(getPosition(i0),getPosition(i1));
} else {
distance=delta(getPosition(i0),getPosition(i1));
}
double dfunc=0.;
ncoord += pairing(distance.modulo2(), dfunc,i0,i1);
deriv[i0] = deriv[i0] + (-dfunc)*distance ;
deriv[i1] = deriv[i1] + dfunc*distance ;
virial=virial+(-dfunc)*Tensor(distance,distance);
}
if(!serial){
comm.Sum(ncoord);
if(!deriv.empty()) comm.Sum(&deriv[0][0],3*deriv.size());
comm.Sum(virial);
}
for(unsigned i=0;i<deriv.size();++i) setAtomsDerivatives(i,deriv[i]);
setValue (ncoord);
setBoxDerivatives (virial);
}
double VolumeTetrapore::calculateNumberInside( const Vector& cpos, Vector& derivatives, Tensor& vir, std::vector<Vector>& rderiv ) const {
// Setup the histogram bead
HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( getKernelType() );
// Calculate distance of atom from origin of new coordinate frame
Vector datom=pbcDistance( origin, cpos );
double ucontr, uder, vcontr, vder, wcontr, wder;
// Calculate contribution from integral along bi
bead.set( 0, len_bi, sigma );
double upos=dotProduct( datom, bi );
ucontr=bead.calculate( upos, uder );
double udlen=bead.uboundDerivative( upos );
double uder2 = bead.lboundDerivative( upos ) - udlen;
// Calculate contribution from integral along cross
bead.set( 0, len_cross, sigma );
double vpos=dotProduct( datom, cross );
vcontr=bead.calculate( vpos, vder );
double vdlen=bead.uboundDerivative( vpos );
double vder2 = bead.lboundDerivative( vpos ) - vdlen;
// Calculate contribution from integral along perp
bead.set( 0, len_perp, sigma );
double wpos=dotProduct( datom, perp );
wcontr=bead.calculate( wpos, wder );
double wdlen=bead.uboundDerivative( wpos );
double wder2 = bead.lboundDerivative( wpos ) - wdlen;
Vector dfd; dfd[0]=uder*vcontr*wcontr; dfd[1]=ucontr*vder*wcontr; dfd[2]=ucontr*vcontr*wder;
derivatives[0] = (dfd[0]*bi[0]+dfd[1]*cross[0]+dfd[2]*perp[0]);
derivatives[1] = (dfd[0]*bi[1]+dfd[1]*cross[1]+dfd[2]*perp[1]);
derivatives[2] = (dfd[0]*bi[2]+dfd[1]*cross[2]+dfd[2]*perp[2]);
double tot = ucontr*vcontr*wcontr*jacob_det;
// Add reference atom derivatives
dfd[0]=uder2*vcontr*wcontr; dfd[1]=ucontr*vder2*wcontr; dfd[2]=ucontr*vcontr*wder2;
Vector dfld; dfld[0]=udlen*vcontr*wcontr; dfld[1]=ucontr*vdlen*wcontr; dfld[2]=ucontr*vcontr*wdlen;
rderiv[0] = dfd[0]*matmul(datom,dbi[0]) + dfd[1]*matmul(datom,dcross[0]) + dfd[2]*matmul(datom,dperp[0]) +
dfld[0]*dlbi[0] + dfld[1]*dlcross[0] + dfld[2]*dlperp[0] - derivatives;
rderiv[1] = dfd[0]*matmul(datom,dbi[1]) + dfd[1]*matmul(datom,dcross[1]) + dfd[2]*matmul(datom,dperp[1]) +
dfld[0]*dlbi[1] + dfld[1]*dlcross[1] + dfld[2]*dlperp[1];
rderiv[2] = dfd[0]*matmul(datom,dbi[2]) + dfd[1]*matmul(datom,dcross[2]) + dfd[2]*matmul(datom,dperp[2]) +
dfld[0]*dlbi[2] + dfld[1]*dlcross[2] + dfld[2]*dlperp[2];
rderiv[3] = dfld[0]*dlbi[3] + dfld[1]*dlcross[3] + dfld[2]*dlperp[3];
vir.zero(); vir-=Tensor( cpos,derivatives );
for(unsigned i=0;i<4;++i){
vir -= Tensor( getPosition(i), rderiv[i] );
}
return tot;
}
void SecondaryStructureRMSD::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
// Retrieve the positions
std::vector<Vector> pos( references[0]->getNumberOfAtoms() );
const unsigned n=pos.size();
for(unsigned i=0;i<n;++i) pos[i]=ActionAtomistic::getPosition( getAtomIndex(current,i) );
// This does strands cutoff
Vector distance=pbcDistance( pos[align_atom_1],pos[align_atom_2] );
if( s_cutoff2>0 ){
if( distance.modulo2()>s_cutoff2 ){
myvals.setValue( 0, 0.0 );
return;
}
}
// This aligns the two strands if this is required
if( alignType!="DRMSD" && align_strands ){
Vector origin_old, origin_new; origin_old=pos[align_atom_2];
origin_new=pos[align_atom_1]+distance;
for(unsigned i=15;i<30;++i){
pos[i]+=( origin_new - origin_old );
}
}
// Create a holder for the derivatives
ReferenceValuePack mypack( 0, pos.size(), myvals ); mypack.setValIndex( 1 );
for(unsigned i=0;i<n;++i) mypack.setAtomIndex( i, getAtomIndex(current,i) );
// And now calculate the RMSD
const Pbc& pbc=getPbc();
unsigned closest=0;
double r = references[0]->calculate( pos, pbc, mypack, false );
const unsigned rs = references.size();
for(unsigned i=1;i<rs;++i){
mypack.setValIndex( i+1 );
double nr=references[i]->calculate( pos, pbc, mypack, false );
if( nr<r ){ closest=i; r=nr; }
}
// Transfer everything to the value
myvals.setValue( 0, 1.0 ); myvals.setValue( 1, r );
if( closest>0 ) mypack.moveDerivatives( closest+1, 1 );
if( !mypack.virialWasSet() ){
Tensor vir;
const unsigned cacs = colvar_atoms[current].size();
for(unsigned i=0;i<cacs;++i){
vir+=(-1.0*Tensor( pos[i], mypack.getAtomDerivative(i) ));
}
mypack.setValIndex(1); mypack.addBoxDerivatives( vir );
}
return;
}
void IMD::calculate(){
if(comm.Get_rank()==0 && connected && plumed.getStep()%transferRate==0 && vmdsock_selwrite(clientsock,0)) {
double scale=10.0*plumed.getAtoms().getUnits().getLength();
Vector ref;
for(int i=0;i<natoms;i++){
Vector pos=getPosition(i);
if(wrap) pos=pbcDistance(ref,pos);
coord[3*i+0]=static_cast<float>((pos[0]*scale));
coord[3*i+1]=static_cast<float>((pos[1]*scale));
coord[3*i+2]=static_cast<float>((pos[2]*scale));
}
imd_send_fcoords(clientsock,natoms,&coord[0]);
}
}
Vector MultiColvarBase::getSeparation( const Vector& vec1, const Vector& vec2 ) const {
if(usepbc){ return pbcDistance( vec1, vec2 ); }
else{ return delta( vec1, vec2 ); }
}
// calculator
void CoordinationBase::calculate()
{
double ncoord=0.;
Tensor virial;
vector<Vector> deriv(getNumberOfAtoms());
// deriv.resize(getPositions().size());
if(nl->getStride()>0 && invalidateList) {
nl->update(getPositions());
}
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if(serial) {
stride=1;
rank=0;
} else {
stride=comm.Get_size();
rank=comm.Get_rank();
}
unsigned nt=OpenMP::getNumThreads();
const unsigned nn=nl->size();
if(nt*stride*10>nn) nt=nn/stride/10;
if(nt==0)nt=1;
#pragma omp parallel num_threads(nt)
{
std::vector<Vector> omp_deriv(getPositions().size());
Tensor omp_virial;
#pragma omp for reduction(+:ncoord) nowait
for(unsigned int i=rank; i<nn; i+=stride) {
Vector distance;
unsigned i0=nl->getClosePair(i).first;
unsigned i1=nl->getClosePair(i).second;
if(getAbsoluteIndex(i0)==getAbsoluteIndex(i1)) continue;
if(pbc) {
distance=pbcDistance(getPosition(i0),getPosition(i1));
} else {
distance=delta(getPosition(i0),getPosition(i1));
}
double dfunc=0.;
ncoord += pairing(distance.modulo2(), dfunc,i0,i1);
Vector dd(dfunc*distance);
Tensor vv(dd,distance);
if(nt>1) {
omp_deriv[i0]-=dd;
omp_deriv[i1]+=dd;
omp_virial-=vv;
} else {
deriv[i0]-=dd;
deriv[i1]+=dd;
virial-=vv;
}
}
#pragma omp critical
if(nt>1) {
for(int i=0; i<getPositions().size(); i++) deriv[i]+=omp_deriv[i];
virial+=omp_virial;
}
}
if(!serial) {
comm.Sum(ncoord);
if(!deriv.empty()) comm.Sum(&deriv[0][0],3*deriv.size());
comm.Sum(virial);
}
for(unsigned i=0; i<deriv.size(); ++i) setAtomsDerivatives(i,deriv[i]);
setValue (ncoord);
setBoxDerivatives (virial);
}