void TorsionConstraint::setup(const AtomSet& atoms) { // find position in tau array corresponding to atom name1 is1_ = atoms.is(name1_); ia1_ = atoms.ia(name1_); assert(is1_>=0); assert(ia1_>=0); m1_ = atoms.species_list[is1_]->mass() * 1822.89; assert(m1_>0.0); m1_inv_ = 1.0 / m1_; is2_ = atoms.is(name2_); ia2_ = atoms.ia(name2_); assert(is2_>=0); assert(ia2_>=0); m2_ = atoms.species_list[is2_]->mass() * 1822.89; assert(m2_>0.0); m2_inv_ = 1.0 / m2_; is3_ = atoms.is(name3_); ia3_ = atoms.ia(name3_); assert(is3_>=0); assert(ia3_>=0); m3_ = atoms.species_list[is3_]->mass() * 1822.89; assert(m3_>0.0); m3_inv_ = 1.0 / m3_; is4_ = atoms.is(name4_); ia4_ = atoms.ia(name4_); assert(is4_>=0); assert(ia4_>=0); m4_ = atoms.species_list[is4_]->mass() * 1822.89; assert(m4_>0.0); m4_inv_ = 1.0 / m4_; }
void PositionConstraint::setup(const AtomSet& atoms) { // find position in tau array corresponding to atom name1 is1_ = atoms.is(name1_); ia1_ = atoms.ia(name1_); assert(is1_>=0); assert(ia1_>=0); }