What is the best practice to read in external geometry files (e.g., pdb, xyz, etc.) with Psi4?
I’ve been using ORCA for some time now and have become interested in using Psi4. There are some flexible and simple ways to read in geometries in multiple ways with ORCA, and this has become an important part of my workflow. However, it doesn’t seem as easy to do in Psi4. As this is my first post here, please excuse my ignorance with the package as a whole. And, of course, thanks in advance for the hand-holding!
To summarize, there is a single mention in the manual and a few answered questions in the forum, but it is still not exactly clear (to me at least) how it should be done. Below, I collated the relevant information I found.
Starting with the manual, reading in a molecular geometry from an external file is placed under “Advanced Python” in an example where two XYZ files are combined for SAPT using the method
Molecule.init_with_xyz. I cannot find any documentation for this method, nor anything else related. Furthermore, it’s confusing having the only mention in the manual mixed up with other instructions rather than providing a simple MWE.
From previous forum posts, the most recent relevant question “Use .xyz file as input coordinate” suggests the use of
Molecule.from_string(xyz_contents_here, dtype='xyz') to read in the files previously opened in a Jupyter Notebook. I do not understand how to read the definition of this class method nor which options it’ll accept. I also do not plan on using a Jupyter notebook, but instead I plan to submit jobs to a cluster with a scheduler, so I suppose this means the XYZ file must be read-in previously as a string, but how?
An older forum post, Some beginner questions, asks the same question, and the asker was directed toward
Molecule.init_with_xyz, too. User loriab explained in more detail how it could be used. This seems like a good starting point for documentation to add to the manual. Is this simply the way to go? Can it be done with other file formats?