void ReferenceAtoms::printAtoms( OFile& ofile, const double& lunits ) const {
plumed_assert( indices.size()==reference_atoms.size() && align.size()==reference_atoms.size() && displace.size()==reference_atoms.size() );
for(unsigned i=0;i<reference_atoms.size();++i){
ofile.printf("ATOM %4d X RES %4u %8.3f%8.3f%8.3f%6.2f%6.2f\n",
indices[i].serial(), i,
lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],
align[i], displace[i] );
}
}
void PointWiseMapping::print( const std::string& method, const double & time, OFile& afile, const std::string& fmt ){
std::string descr2, descr="DESCRIPTION: results from %s analysis performed at time " + fmt +"\n";
afile.printf(descr.c_str(), method.c_str(), time );
if(fmt.find("-")!=std::string::npos){
descr="REMARK WEIGHT=" + fmt + " %s=" + fmt + " "; descr2="%s=" + fmt;
} else {
// This ensures numbers are left justified (i.e. next to the equals sign
std::size_t psign=fmt.find("%");
plumed_assert( psign!=std::string::npos );
descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + " %s=%-" + fmt.substr(psign+1) + " ";
descr2="%s=%-" + fmt.substr(psign+1);
}
for(unsigned i=0;i<frames.size();++i){
afile.printf(descr.c_str(), frames[i]->getWeight(), property[0].c_str(), low_dim[i][0] );
for(unsigned j=1;j<property.size();++j) afile.printf(descr2.c_str(), property[j].c_str(), low_dim[i][j]);
afile.printf("\n");
frames[i]->print( afile, fmt );
}
}