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.

Sign up for GitHub

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

Jump to bottom

Add Gaussian harness #442

Open
wants to merge 23 commits into
base: master
Choose a base branch
from
Open

Add Gaussian harness #442

wants to merge 23 commits into from

Conversation

QuChem
Copy link

@QuChem QuChem commented Feb 14, 2024

Description

This is the implementation of Gaussian software into QCEngine

@codecov Codecov
Copy link

codecov bot commented Feb 14, 2024 •
edited
Loading

Codecov Report

Attention: Patch coverage is 0% with 191 lines in your changes missing coverage. Please review.

Project coverage is 78.18%. Comparing base (1b27a14) to head (aad52cf).
Report is 7 commits behind head on master.

❗ Current head aad52cf differs from pull request most recent head a2ff5c8

Please upload reports for the commit a2ff5c8 to get more accurate results.

Additional details and impacted files

github-advanced-security[bot]
github-advanced-security bot found potential problems Feb 14, 2024
View reviewed changes
qcengine/programs/gaussian.py
Comment on lines +128 to +129
#if input_model.molecule.fix_com or input_model.molecule.fix_orientation:
# keywords["SYM_IGNORE"] = "TRUE"

Check notice

Code scanning / CodeQL

Commented-out code Note

This comment appears to contain commented-out code.
qcengine/programs/gaussian.py
Comment on lines +207 to +209
#if input_model.driver == 'energy':
# print (cclib.__version__)
# print (output_data)

Check notice

Code scanning / CodeQL

Commented-out code Note

This comment appears to contain commented-out code.
qcengine/programs/gaussian.py
"""

import os
import re

Check notice

Code scanning / CodeQL

Unused import Note

Import of 're' is not used.
qcengine/programs/gaussian.py

import os
import re
import tempfile

Check notice

Code scanning / CodeQL

Unused import Note

Import of 'tempfile' is not used.
qcengine/programs/gaussian.py
import os
import re
import tempfile
import warnings

Check notice

Code scanning / CodeQL

Unused import Note

Import of 'warnings' is not used.
qcengine/programs/gaussian.py
data = cclib.io.ccread(tmp_output_file)
cclib_vars = data.getattributes(True)

last_occupied_energy = data.moenergies[0][data.homos[0]]

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable last_occupied_energy is not used.
qcengine/programs/gaussian.py Fixed Show fixed Hide fixed
qcengine/programs/gaussian.py

provenance = Provenance(creator="Gaussian", version=self.get_version(), routine='g09').dict()

stdout = outfiles.pop('stdout')

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable stdout is not used.
qcengine/programs/gaussian.py
provenance = Provenance(creator="Gaussian", version=self.get_version(), routine='g09').dict()

stdout = outfiles.pop('stdout')
stderr = outfiles.pop('stderr')

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable stderr is not used.
qcengine/programs/gaussian.py
#print("\nPRINT STDOUT: \n", stdout)


method = input_model.model.method.lower()

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable method is not used.
@bennybp bennybp changed the title QuChem gaussian added Add Gaussian harness Feb 14, 2024
@bennybp
Copy link
Collaborator

bennybp commented Feb 16, 2024

I think programs.py should be base.py inside the programs folder. You should modify that file with your changes

github-advanced-security[bot]
github-advanced-security bot found potential problems Mar 14, 2024
View reviewed changes
qcengine/programs/gaussian.py
output_data['success'] = True
#print ('output_data: ', output_data)

provenance = Provenance(creator="gaussian", version=self.get_version(), routine='g09').dict()

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable provenance is not used.
loriab
loriab reviewed May 2, 2024
View reviewed changes
Copy link
Collaborator

@loriab loriab left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for working on this! Here's some initial queries.

qcengine/programs/gaussian.py Show resolved Hide resolved
qcengine/programs/gaussian.py
#if input_model.molecule.fix_com or input_model.molecule.fix_orientation:
# keywords["SYM_IGNORE"] = "TRUE"
if 'SCF_CONVERGENCE' in keywords:
gaussian_kw.append('SCF=' + keywords["SCF_CONVERGENCE"])
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Where is the name "SCF_CONVERGENCE" coming from? QCNG tends to want the same keyword names in AtIn.keywords as the experience user would use in the program natively. Is Conver=N on https://gaussian.com/scf/ ("Options" tab) what you're targeting?

qcengine/programs/gaussian.py Show resolved Hide resolved
qcengine/programs/gaussian.py Show resolved Hide resolved
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@loriab loriab loriab left review comments

At least 1 approving review is required to merge this pull request.

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@QuChem @bennybp @loriab