Dear program developers,
Recently, I write some codes based on Psi4 API module. I met some questions, and I hope you can help me.
I created a molecule like this,
mole = “”"
C -1.86708863 0.79113923 0.00000000
H -1.51043420 -0.21767077 0.00000000
H -1.51041579 1.29553742 0.87365150
H -1.51041579 1.29553742 -0.87365150
H -2.93708863 0.79115241 0.00000000
mol = psi4.geometry(mole)
xyzGeom = np.array(mol.geometry())
NAtom = mol.natom()
R = np.zeros((NAtom, NAtom), np.double)
for i, j in combinations(range(NAtom), 2):
R[i,j] = R[j,i] = v3d.dist(xyzGeom[i], xyzGeom[j])
Next, I print the distance matrix using the codes written by me:
***** Distance Matrix *****
0 1 2 3 4
1 1.070000E+00 0.000000E+00
2 1.070000E+00 1.747302E+00 0.000000E+00
3 1.070000E+00 1.747302E+00 1.747303E+00 0.000000E+00
4 1.070000E+00 1.747303E+00 1.747303E+00 1.747303E+00 0.000000E+00
I noticed that the units of the distance matrix is angstrom and the matrix elements are same as output of Gaussian program. In fact, if I don’t use keywords “units bohr” in my mole input, the output is wrong. However, the default unit of the distance is angstrom in Psi4.
I am very confused about this and hope that you can answer it.
Thanks a lot,