Farnaz Heidar-Zadeh

Results 38 comments of Farnaz Heidar-Zadeh

@BradenDKelly I encountered the problem a few weeks ago. This happens because `iodata` first tries to identify the element (and atomic numbers) from columns 77-78 which is empty in your...

@nwoodweb thanks for your contributions. As shared in issue #269, having a test for every line of code is part of our contribution guidelines, so we cannot review your PR...

@fwmeng88 actually, I was just needing to get some geometry information out of the Gaussian log file, so it would be very useful to parse more information out of the...

@evohringer and @tovrstra can you please decide what to do with these formats left from `molmod`: https://github.com/molmod/molmod/tree/master/molmod/io 1. `atrj` 2. `cml` 3. `cpmd` 4. `crystal` 5. `dlpoly` 6. `gamess` 7....

@evohringer I understand that PDB is a better format (well-defined and versatile), but if I am not wrong, there is information in the output files that are not printed in...

@RichRick1 please take a look at `gamess` format in `molmod` which needs to be transferred to `iodata` and be added in `iodata/formats` module. Thanks. https://github.com/molmod/molmod/blob/master/molmod/io/gamess.py

@nwoodweb thanks for working on this issue. Please follow our contributing guidelines https://iodata.readthedocs.io/en/latest/contributing.html in preparing your PR.

I have been working on `iodata` all day today trying to improve it, and I think its `overlap` code is over-complicated and even out of place to some extent. If...

I am implementing a simple and easy to understand `compute_overlap` function based on @PaulWAyers notes. It seems to be pretty efficient, so it may not even need to be Cythonized...

@tovrstra I mihgt be missing sth, but didn't we decide to represent `shells` as a list of namedtuple('Shell', ['icenter', 'iatom', 'angmoms', 'exponents', 'contractions'])?