Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix a bug with parsing ORCA orbital coefficients #1910

Merged
merged 1 commit into from
Jan 4, 2025

Conversation

ghutchis
Copy link
Member

@ghutchis ghutchis commented Jan 4, 2025

Ensure orbital reordering is handled correctly
Fixes https://discuss.avogadro.cc/t/molecular-orbitals-displayed-incorrectly/6675?u=ghutchis As reported by forum user chem.os

Developer Certificate of Origin
Version 1.1

Copyright (C) 2004, 2006 The Linux Foundation and its contributors.
1 Letterman Drive
Suite D4700
San Francisco, CA, 94129

Everyone is permitted to copy and distribute verbatim copies of this
license document, but changing it is not allowed.

Developer's Certificate of Origin 1.1

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I
have the right to submit it under the open source license
indicated in the file; or

(b) The contribution is based upon previous work that, to the best
of my knowledge, is covered under an appropriate open source
license and I have the right under that license to submit that
work with modifications, whether created in whole or in part
by me, under the same open source license (unless I am
permitted to submit under a different license), as indicated
in the file; or

(c) The contribution was provided directly to me by some other
person who certified (a), (b) or (c) and I have not modified
it.

(d) I understand and agree that this project and the contribution
are public and that a record of the contribution (including all
personal information I submit with it, including my sign-off) is
maintained indefinitely and may be redistributed consistent with
this project or the open source license(s) involved.

Ensure orbital reordering is handled correctly
Fixes https://discuss.avogadro.cc/t/molecular-orbitals-displayed-incorrectly/6675?u=ghutchis
As reported by forum user chem.os

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
@avo-bot
Copy link

avo-bot commented Jan 4, 2025

This pull request has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/molecular-orbitals-displayed-incorrectly/6675/4

getline(in, key);
key_begin = std::sregex_iterator(key.begin(), key.end(), rx);
key_end = std::sregex_iterator();
auto key_begin = std::sregex_iterator(key.begin(), key.end(), rx);

Check notice

Code scanning / CodeQL

Declaration hides variable Note

Variable key_begin hides another variable of the same name (on
line 953
).
key_begin = std::sregex_iterator(key.begin(), key.end(), rx);
key_end = std::sregex_iterator();
auto key_begin = std::sregex_iterator(key.begin(), key.end(), rx);
auto key_end = std::sregex_iterator();

Check notice

Code scanning / CodeQL

Declaration hides variable Note

Variable key_end hides another variable of the same name (on
line 954
).
Copy link
Contributor

github-actions bot commented Jan 4, 2025

Here are the build results
Ubuntu-Latest.tar.gz
Avogadro2.AppImage
macOS.dmg
Win64.exe
Artifacts will only be retained for 90 days.

@chem-os
Copy link

chem-os commented Jan 4, 2025

I've tested the Windows version, the MOs are displayed correctly now. Thank you!

@ghutchis ghutchis merged commit acae593 into OpenChemistry:master Jan 4, 2025
23 checks passed
@ghutchis ghutchis deleted the fixup-orca-orbital-parsing branch January 4, 2025 15:48
@ghutchis
Copy link
Member Author

ghutchis commented Jan 4, 2025

Thanks for reporting the bug!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants