void BridgeVessel::completeNumericalDerivatives(){
unsigned nextra = myOutputAction->getNumberOfDerivatives() - getAction()->getNumberOfDerivatives();
Matrix<double> tmpder( myOutputValues->getNumberOfComponents(), nextra );
ActionWithVessel* vval=dynamic_cast<ActionWithVessel*>( myOutputAction );
for(unsigned i=0;i<nextra;++i){
vval->bridgeVariable=i; getAction()->calculate();
for(int j=0;j<myOutputValues->getNumberOfComponents();++j) tmpder(j,i) = myOutputValues->getOutputQuantity(j);
}
vval->bridgeVariable=nextra; getAction()->calculate();
plumed_assert( inum==mynumerical_values.size() ); inum=0; // Reset inum now that we have finished calling calculate
std::vector<double> base( myOutputValues->getNumberOfComponents() );
for(int j=0;j<myOutputValues->getNumberOfComponents();++j) base[j] = myOutputValues->getOutputQuantity(j);
const double delta=sqrt(epsilon);
ActionAtomistic* aa=dynamic_cast<ActionAtomistic*>( getAction() );
unsigned nvals=myOutputValues->getNumberOfComponents();
for(unsigned j=0;j<nvals;++j) ( myOutputValues->copyOutput(j) )->clearDerivatives();
if( aa ){
ActionWithArguments* aarg=dynamic_cast<ActionWithArguments*>( getAction() );
plumed_assert( !aarg ); Tensor box=aa->getBox();
unsigned natoms=aa->getNumberOfAtoms();
for(unsigned j=0;j<nvals;++j){
double ref=( myOutputValues->copyOutput(j) )->get();
if( ( myOutputValues->copyOutput(j) )->getNumberOfDerivatives()>0 ){
for(unsigned i=0;i<3*natoms;++i){
double d=( mynumerical_values[i*nvals+j] - ref)/delta;
( myOutputValues->copyOutput(j) )->addDerivative(i,d);
}
Tensor virial;
for(int i=0;i<3;i++) for(int k=0;k<3;k++){
virial(i,k)=( mynumerical_values[ nvals*(3*natoms + 3*i + k) + j ]-ref)/delta;
}
virial=-matmul(box.transpose(),virial);
for(int i=0;i<3;i++) for(int k=0;k<3;k++) ( myOutputValues->copyOutput(j) )->addDerivative(3*natoms+3*k+i,virial(k,i));
}
}
} else {
plumed_merror("not implemented or tested yet");
// unsigned nder=myOutputAction->getNumberOfDerivatives();
// for(unsigned j=0;j<nvals;++j){
// double ref=( myOutputValues->copyOutput(j) )->get();
// for(unsigned i=0;i<nder;++i){
// double d=( mynumerical_values[i*nvals+j] - ref)/delta;
// ( myOutputValues->copyOutput(j) )->addDerivative(i,d);
// }
// }
// }
}
// Add the derivatives wrt to the local quantities we are working with
for(unsigned j=0;j<nvals;++j){
unsigned k=0;
for(unsigned i=getAction()->getNumberOfDerivatives();i<myOutputAction->getNumberOfDerivatives();++i){
( myOutputValues->copyOutput(j) )->addDerivative( i, (tmpder(j,k)-base[j])/sqrt(epsilon) ); k++;
}
}
}
void Molecular_system::locDerivative(int ion, Sample_point * sample,
Force_fitter & fitter,
Array1 <doublevar> & der) {
sample->updateEIDist();
der.Resize(3);
der=0;
Array1 <doublevar> R(5);
int ne=sample->electronSize();
Array1 <doublevar> tmpder(3), tmpder_fit(3);
for(int e=0; e< ne; e++) {
sample->getEIDist(e,ion, R);
for(int d=0; d< 3; d++)
//der(d)-=sample->getIonCharge(ion)*R(d+2)/(R(1)*R(0));
tmpder(d)=-sample->getIonCharge(ion)*R(d+2)/(R(1)*R(0));
fitter.fit_force(R,tmpder, tmpder_fit);
for(int d=0; d< 3; d++)
der(d)+=tmpder_fit(d);
}
Array1 <doublevar> vec(3);
Array1 <doublevar> r_ion(3);
sample->getIonPos(ion, r_ion);
int nIon=sample->ionSize();
for(int j=0; j< nIon; j++) {
if(j!=ion) {
sample->getIonPos(j,R);
doublevar r2=0;
for(int d=0; d <3; d++)
vec(d)=r_ion(d)-R(d);
for(int d=0; d< 3; d++)
r2+=vec(d)*vec(d);
doublevar r=sqrt(r2);
for(int d=0; d< 3; d++)
der(d)-=sample->getIonCharge(ion)*sample->getIonCharge(j)*vec(d)/(r2*r);
}
}
}
void BiasRepresentation::pushKernel( IFile *ifile ){
KernelFunctions *kk;
// here below the reading of the kernel is completely hidden
if(histosigma.size()==0){
ifile->allowIgnoredFields();
kk=KernelFunctions::read(ifile,names) ;
}else{
// when doing histogram assume gaussian with a given diagonal sigma
// and neglect all the rest
kk=readFromPoint(ifile) ;
}
hills.push_back(kk);
// the bias factor is not something about the kernels but
// must be stored to keep the bias/free energy duality
string dummy; double dummyd;
if(ifile->FieldExist("biasf")){
ifile->scanField("biasf",dummy);
Tools::convert(dummy,dummyd);
}else{dummyd=1.0;}
biasf.push_back(dummyd);
// the domain does not pertain to the kernel but to the values here defined
string mins,maxs,minv,maxv,mini,maxi;mins="min_";maxs="max_";
for(int i=0 ; i<ndim; i++){
if(values[i]->isPeriodic()){
ifile->scanField(mins+names[i],minv);
ifile->scanField(maxs+names[i],maxv);
// verify that the domain is correct
values[i]->getDomain(mini,maxi);
plumed_massert(mini==minv,"the input periodicity in hills and in value definition does not match" );
plumed_massert(maxi==maxv,"the input periodicity in hills and in value definition does not match" );
}
}
// if grid is defined then it should be added on the grid
//cerr<<"now with "<<hills.size()<<endl;
if(hasgrid){
vector<unsigned> nneighb=kk->getSupport(BiasGrid_->getDx());
vector<unsigned> neighbors=BiasGrid_->getNeighbors(kk->getCenter(),nneighb);
vector<double> der(ndim);
vector<double> xx(ndim);
if(mycomm.Get_size()==1){
for(unsigned i=0;i<neighbors.size();++i){
unsigned ineigh=neighbors[i];
for(int j=0;j<ndim;++j){der[j]=0.0;}
BiasGrid_->getPoint(ineigh,xx);
// assign xx to a new vector of values
for(int j=0;j<ndim;++j){values[j]->set(xx[j]);}
double bias=kk->evaluate(values,der,true);
if(rescaledToBias){
double f=(biasf.back()-1.)/(biasf.back());
bias*=f;
for(int j=0;j<ndim;++j){der[j]*=f;}
}
BiasGrid_->addValueAndDerivatives(ineigh,bias,der);
}
} else {
unsigned stride=mycomm.Get_size();
unsigned rank=mycomm.Get_rank();
vector<double> allder(ndim*neighbors.size(),0.0);
vector<double> allbias(neighbors.size(),0.0);
vector<double> tmpder(ndim);
for(unsigned i=rank;i<neighbors.size();i+=stride){
unsigned ineigh=neighbors[i];
BiasGrid_->getPoint(ineigh,xx);
for(int j=0;j<ndim;++j){values[j]->set(xx[j]);}
allbias[i]=kk->evaluate(values,tmpder,true);
if(rescaledToBias){
double f=(biasf.back()-1.)/(biasf.back());
allbias[i]*=f;
for(int j=0;j<ndim;++j){tmpder[j]*=f;}
}
// this solution with the temporary vector is rather bad, probably better to take
// a pointer of double as it was in old gaussian
for(int j=0;j<ndim;++j){ allder[ndim*i+j]=tmpder[j];tmpder[j]=0.;}
}
mycomm.Sum(allbias);
mycomm.Sum(allder);
for(unsigned i=0;i<neighbors.size();++i){
unsigned ineigh=neighbors[i];
for(int j=0;j<ndim;++j){der[j]=allder[ndim*i+j];}
BiasGrid_->addValueAndDerivatives(ineigh,allbias[i],der);
}
}
}
}
