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CFOUR molden files #273
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Thanks for pointing this out. @tovrstra is probably the best person to respond in detail. As you've surmised, molden files are darn tricky. Just off hand, however, I don't think it will be that difficult to support CFOUR molden files too. |
@shivupa Thanks for bringing this up. We'd love to update our code so it can handle CFOUR files. How familiar are you with changing the source code and making a pull request? We typically review PRs and make suggestions for code improvements until it all looks good. A good start is to create a PR with unit tests with CFOUR files, which just show that the current code fails. Then you can add commits to fix the problems. A technically detailed outline can be found here: https://github.com/theochem/iodata/blob/master/CONTRIBUTING.rst I took a quick look at the molden file in the gist and this one is certainly useful for unit testing, i.e. it is not too big. It will take a bit of reverse engineering to find out the non-standard conventions that CFOUR Molden files use. By calculating and printing out the overlap matrix with IOData of the MO's for a small calculation, like you provide, you can detect where the issues are. This should obviously be an identity matrix, but this fails when there is a mismatch with the conventions. An example of such a test can found here: iodata/iodata/test/test_molden.py Lines 263 to 281 in 1de4661
The function The function with all the fixes for buggy molden files can be found here: iodata/iodata/formats/molden.py Line 552 in 1de4661
Depending on the type of issues in the Molden file, you may need to fix the sign convention, the ordering of the basis functions (within each shell) and/or their normalization. Non-standard signs and orderings can be defined in a I'm not sure if this answer your question? |
@tovrstra thanks for orienting us and giving us some guidance, it's very helpful Your response has answered all of the questions we have at this point. We are familiar with python development with git and github, so this will be fine for us. We will open a WIP pull request and get started! |
Closed via #276 |
Hi,
We have noticed the MOs printed in the CFOUR MOLDEN output are not normalized as expected. We were interested in standardizing this.
We summarize the quirks below (relevant files are at this gist):
We have run zero electron calculations with d,f,g,h functions individually to assist with the normalization and ordering. Could you recommend a path forward to get the properly normalized MOLDENs out? We are willing to help as much as we can since this is critical for our research.
Thanks,
Shiv Upadhyay (@shivupa) and Amanda Dumi (@amandadumi)
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