I define this structure:
struct s_molecule
{
std::string res_name;
std::vector<t_particle> my_particles;
std::vector<t_bond> my_bonds;
std::vector<t_angle> my_angles;
std::vector<t_dihedral> my_dihedrals;
s_molecule& operator=(const s_molecule &to_assign)
{
res_name = to_assign.res_name;
my_particles = to_assign.my_particles;
my_bonds = to_assign.my_bonds;
my_angles = to_assign.my_angles;
my_dihedrals = to_assign.my_dihedrals;
return *this;
}
};
and these structures:
typedef struct s_particle
{
t_coordinates position;
double charge;
double mass;
std::string name;
std::vector<t_lj_param>::iterator my_particle_kind_iter;
s_particle& operator=(const s_particle &to_assign)
{
position = to_assign.position;
charge = to_assign.charge;
mass = to_assign.mass;
name = to_assign.name;
my_particle_kind_iter = to_assign.my_particle_kind_iter;
return *this;
}
} t_particle;
struct s_bond
{
t_particle * particle_1;
t_particle * particle_2;
std::vector<t_bond_param>::iterator my_bond_kind_iter;
s_bond& operator=(const s_bond &to_assign)
{
particle_1 = to_assign.particle_1;
particle_2 = to_assign.particle_2;
my_bond_kind_iter = to_assign.my_bond_kind_iter;
return *this;
}
};
and then in my code I return a pointer to an s_molecule (typedef'd to t_molecule, but still).
Using this pointer I can get this code to work:
for (unsigned int i = 0;
i < current_molecule->my_particles.size();
i++)
{
std::cout << "Particle "
<< current_molecule->my_particles[i].name << std::endl
<< "Charge: "
<< current_molecule->my_particles[i].charge << std::endl
<< "Mass: "
<< current_molecule->my_particles[i].mass << std::endl
<< "Particle Kind Name: "
<< (*current_molecule->my_particles[i].my_particle_kind_iter).atom_kind_name
<< std::endl
<< "x: " << current_molecule->my_particles[i].position.x
<< " y: " << current_molecule->my_particles[i].position.y
#ifdef USE_3D_GEOM
<< "z: " << current_molecule->my_particles[i].position.z
#endif
<< std::endl;
}
If I replace it with:
for (std::vector<t_particle>::iterator it = current_molecule->my_particles.begin();
it !=current_molecule->my_particles.end();
it++)
{
std::cout << "Particle "
<< (*it).name << std::endl
<< "Charge: "
<< (*it).charge << std::endl
<< "Mass: "
<< (*it).mass << std::endl
<< "Particle Kind Name: "
<< (*(*it).my_particle_kind_iter).atom_kind_name
<< std::endl
<< "x: " << (*it).position.x
<< " y: " << (*it).position.y
#ifdef USE_3D_GEOM
<< "z: " << (*it).position.z
#endif
<< std::endl;
}
I now get nasty segfaults...
Not to put too much here, but I'm also getting segfaults when I tried to do this:
std::cout << "Bond ATOMS : "
<< (*current_molecule).my_bonds[0].particle_1->name
<< std::endl
Again, current_molecule is a pointer to a s_molecule structure, which contains arrays of structures, which in turn either directly have vars or are pointers. I can't get these multiple layers of indirection to work. Suggestions on fixing these segfaults.
FYI I'm compiling on Linux Centos 5.4 with g++ and using a custom makefile system.
Again, this issue was answered here: Weird Pointer issue in C++ by DeadMG. Sorry for the double post.