search

patonlab / GoodVibes

Calculate quasi-harmonic free energies from Gaussian output files with temperature and other corrections
http://www.patonlab.colostate.edu
MIT License
129 stars 50 forks source link

mismatch in --check in v3.2 #65

Open turkiAlturaifi opened 1 year ago

turkiAlturaifi commented 1 year ago

There seems to be an issue with the --check in v3.2. It gives the following output: x Caution! Potential differences found between frequency and single-point geometries

The geometries are the same and using --check in v3.0.2 doesn't give this warning. Thanks!

npe1011 commented 5 months ago

I have encountered the same issues. It seems that, with the current version, the geometry of the first strcuture is read instead of the last structure. So in case opt+freq is run, the structure mismatch may occur. The file io part seems to have been much charnged from ver 3.02.

Probably the follwing part.

getoutData class in io.py 

# Assuming that the output file doesn't contain a geometry
# optimization at the beginning, we take the first set of atomic
# coordinates rather than the last, in the even that a finite
# difference frequency calculation was performed and the displaced
# geometries are printed.
self.cartesians = data.atomcoords[0].tolist()
npe1011 commented 5 months ago

This issue is also affecting --xyz option. The first structures, often unoptimized, are saved.