step2-solution.md

Here we use the Molecule class we've been working on so far, and thanks to the new "bond()" function, we don't need to worry about storing the distances in a matrix:

#include "molecule.h"
#include <iostream>
#include <fstream>
#include <iomanip>
#include <cstdio>
#include <cmath>

using namespace std;
 
int main()
{
  Molecule mol("geom.dat", 0);
 
  cout << "Number of atoms: " << mol.natom << endl;
  cout << "Input Cartesian coordinates:\n";
  mol.print_geom();
 
  cout << "Interatomic distances (bohr):\n";
  for(int i=0; i < mol.natom; i++)
    for(int j=0; j < i; j++)
      printf("%d %d %8.5f\n", i, j, mol.bond(i,j));
      
  return 0;
}

The output from the above program for the acetaldehyde test case is:

Number of atoms: 7
Input Cartesian coordinates:
6       0.000000000000       0.000000000000       0.000000000000
6       0.000000000000       0.000000000000       2.845112131228
8       1.899115961744       0.000000000000       4.139062527233
1      -1.894048308506       0.000000000000       3.747688672216
1       1.942500819960       0.000000000000      -0.701145981971
1      -1.007295466862      -1.669971842687      -0.705916966833
1      -1.007295466862       1.669971842687      -0.705916966833
Interatomic distances (bohr):
1 0  2.84511
2 0  4.55395
2 1  2.29803
3 0  4.19912
3 1  2.09811
3 2  3.81330
4 0  2.06517
4 1  4.04342
4 2  4.84040
4 3  5.87463
5 0  2.07407
5 1  4.05133
5 2  5.89151
5 3  4.83836
5 4  3.38971
6 0  2.07407
6 1  4.05133
6 2  5.89151
6 3  4.83836
6 4  3.38971
6 5  3.33994