4
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what is the best way to save and load a psi4 molecule? I tried pickle/dill but they both failed. I see a feature to save as xyz, but I'm not seeing a function to load as xyz and I'm not sure if save xyz also saves the energy and charges etc.

import psi4

# Define the molecular geometry using a string
h2_geometry = """
H 0.0 0.0 0.0
H 0.0 0.0 0.74
"""

# Create the molecule object
h2_molecule = psi4.geometry(h2_geometry)
pickle_file_path = "psi4_mol.pkl"
with open(pickle_file_path, 'wb') as file:
    pickle.dump(h2_molecule, file)

Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
TypeError: cannot pickle 'psi4.core.Molecule' object

I also tried dill:

with open(pickle_file_path, 'wb') as file:
    dill.dump(h2_molecule, file)

Traceback (most recent call last):
  File "<stdin>", line 2, in <module>
  File "lib/python3.11/site-packages/dill/_dill.py", line 250, in dump
    Pickler(file, protocol, **_kwds).dump(obj)
  File "lib/python3.11/site-packages/dill/_dill.py", line 418, in dump
    StockPickler.dump(self, obj)
  File "lib/python3.11/pickle.py", line 487, in dump
    self.save(obj)
  File "lib/python3.11/site-packages/dill/_dill.py", line 412, in save
    StockPickler.save(self, obj, save_persistent_id)
  File "lib/python3.11/pickle.py", line 560, in save
    f(self, obj)  # Call unbound method with explicit self
    ^^^^^^^^^^^^
  File "lib/python3.11/pickle.py", line 887, in save_tuple
    save(element)
  File "lib/python3.11/site-packages/dill/_dill.py", line 412, in save
    StockPickler.save(self, obj, save_persistent_id)
  File "lib/python3.11/pickle.py", line 578, in save
    rv = reduce(self.proto)
         ^^^^^^^^^^^^^^^^^^
TypeError: cannot pickle 'psi4.core.Molecule' object
```
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    $\begingroup$ You may find the Psikit functions useful (github.com/Mishima-syk/psikit/blob/master/psikit/psikit.py). The GitHub repo hasn't been updated in quite some time, but the functions are pretty easily replicated (I'm planning to fork an update soon that plugs into py3Dmol on the other end). $\endgroup$ Oct 24, 2023 at 21:18
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    $\begingroup$ Yes it's really interesting especially how it is integrating RDKit with Psi4, I was having trouble passing Psi4 to RDKit also. Thanks I will check it out! $\endgroup$
    – Frank
    Oct 26, 2023 at 12:45

1 Answer 1

5
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If you only need the geometry, molecular charge, and other related quantities, then h2_geometry.to_dict() is what you want. You can then save the returned dict with e.g. pickle.

If you also want to compute energies and such then save them to file, you want wfn.to_file and the partner function for loading, wfn.from_file. These functions also generate (and read) dicts, which are serialized forms of the entire wavefunction. You may also pass an optional filename, which will save the wavefunction object as a numpy file.

You can get the wavefunction as a return from a calculation or building it yourself, e.g.

import psi4

mol = psi4.geometry("""
H 0.0 0.0 0.0
H 0.0 0.0 0.74""")

# build wfn yourself
bas = psi4.core.BasisSet.build(mol,"ORBITAL","sto-3g",quiet=True)
wfn = psi4.core.Wavefunction(mol,bas)

# get wfn as a return
psi4.set_options({"basis":"sto-3g"})
e,wfn = psi4.energy('scf',return_wfn=True)

# either way, save to file
wfn.to_file('wfn.npy')

# load it back up as a new wfn and print the variables inside
new_wfn = psi4.core.Wavefunction.from_file('wfn.npy')
print(new_wfn.variables())
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  • $\begingroup$ But then how to reload it? I'm trying to save it so that I can come back to it later. If you append your answer to reload the psi4 from the file, I'll mark it correct. $\endgroup$
    – Frank
    Oct 30, 2023 at 18:44
  • $\begingroup$ @Frank I believe that would just be the psi4.core.Wavefunction.from_file that Ben links to in their answer. $\endgroup$
    – Tyberius
    Oct 31, 2023 at 13:01
  • $\begingroup$ yes, from_file is what you need. I've added that to the answer. $\endgroup$
    – Ben Peyton
    Nov 1, 2023 at 20:09

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