void CoeffsBase::writeCoeffsInfoToFile(OFile& ofile) const {
ofile.addConstantField(field_type_).printField(field_type_,getTypeStr());
ofile.addConstantField(field_ndimensions_).printField(field_ndimensions_,(int) numberOfDimensions());
ofile.addConstantField(field_ncoeffs_total_).printField(field_ncoeffs_total_,(int) numberOfCoeffs());
for(unsigned int k=0; k<numberOfDimensions(); k++) {
ofile.addConstantField(field_shape_prefix_+getDimensionLabel(k));
ofile.printField(field_shape_prefix_+getDimensionLabel(k),(int) shapeOfIndices(k));
}
}
void MetaD::writeGaussian(const Gaussian& hill, OFile&file){
unsigned ncv=getNumberOfArguments();
file.printField("time",getTimeStep()*getStep());
for(unsigned i=0;i<ncv;++i){
file.printField(getPntrToArgument(i),hill.center[i]);
}
if(hill.multivariate){
hillsOfile_.printField("multivariate","true");
Matrix<double> mymatrix(ncv,ncv);
unsigned k=0;
for(unsigned i=0;i<ncv;i++){
for(unsigned j=i;j<ncv;j++){
mymatrix(i,j)=mymatrix(j,i)=hill.sigma[k]; // recompose the full inverse matrix
k++;
}
}
// invert it
Matrix<double> invmatrix(ncv,ncv);
Invert(mymatrix,invmatrix);
// enforce symmetry
for(unsigned i=0;i<ncv;i++){
for(unsigned j=i;j<ncv;j++){
invmatrix(i,j)=invmatrix(j,i);
}
}
// do cholesky so to have a "sigma like" number
Matrix<double> lower(ncv,ncv);
cholesky(invmatrix,lower); // now this , in band form , is similar to the sigmas
// loop in band form
for (unsigned i=0;i<ncv;i++){
for (unsigned j=0;j<ncv-i;j++){
file.printField("sigma_"+getPntrToArgument(j+i)->getName()+"_"+getPntrToArgument(j)->getName(),lower(j+i,j));
}
}
} else {
hillsOfile_.printField("multivariate","false");
for(unsigned i=0;i<ncv;++i)
file.printField("sigma_"+getPntrToArgument(i)->getName(),hill.sigma[i]);
}
double height=hill.height;
if(welltemp_){height*=biasf_/(biasf_-1.0);}
file.printField("height",height).printField("biasf",biasf_);
if(mw_n_>1) file.printField("clock",int(time(0)));
file.printField();
}
void MaxEnt::WriteLagrangians(vector<double> &lagmult,OFile &file) {
if(printFirstStep) {
unsigned ncv=getNumberOfArguments();
file.printField("time",getTimeStep()*getStep());
for(unsigned i=0; i<ncv; ++i)
file.printField(getPntrToArgument(i)->getName()+"_coupling",lagmult[i]);
file.printField();
} else {
if(!isFirstStep) {
unsigned ncv=getNumberOfArguments();
file.printField("time",getTimeStep()*getStep());
for(unsigned i=0; i<ncv; ++i)
file.printField(getPntrToArgument(i)->getName()+"_coupling",lagmult[i]);
file.printField();
}
}
}