Not generating .hdf5 file

[raghavven]

Hi All,

The molecular data class is not generating .hdf5 file in the location it says it has created one. For e.g. I am running the following code. from openfermion.chem import MolecularData

Set parameters to make a simple molecule.

diatomic_bond_length = .7414 geometry = [('H', (0., 0., 0.)), ('H', (0., 0., diatomic_bond_length))] basis = 'sto-3g' multiplicity = 1 charge = 0 description = str(diatomic_bond_length)

Make molecule and print out a few interesting facts about it.

molecule = MolecularData(geometry, basis, multiplicity, charge, description) print('Molecule has automatically generated name {}'.format( molecule.name)) print('Information about this molecule would be saved at:\n{}\n'.format( molecule.filename)) print('This molecule has {} atoms and {} electrons.'.format( molecule.n_atoms, molecule.n_electrons)) for atom, atomic_number in zip(molecule.atoms, molecule.protons): print('Contains {} atom, which has {} protons.'.format( atom, atomic_number))

And then it prints in the jupyter notebook saying the following """ Molecule has automatically generated name H2_sto-3g_singlet_0.7414 Information about this molecule would be saved at: /home/subbu/psi4conda/envs/penny/lib/python3.8/site-packages/openfermion/testing/data/H2_sto-3g_singlet_0.7414

This molecule has 2 atoms and 2 electrons. Contains H atom, which has 1 protons. Contains H atom, which has 1 protons.

_However, when I see the path , there is no such file listed there. Can you kindly help me troubleshoot the error.

Thank you._

[ncrubin]

Hi @raghavven, could you try saving it outside your site-packages and python directory? Maybe to some random directory in your home? I am wondering if there is a permissions issue here.

[ncrubin]

Actually, it is because the save method is not called. For your molecule to show up in that directory you can call molecule.save() which will write the hdf5 file.

[raghavven]

Thanks so much for your reply @ncrubin . It worked.