New Gaussian plugin #325
New Gaussian plugin #325
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it would be great if the tests could be refactored to not need large test files. 16MB files increase the git clone for future contributors
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I just replaced the files that are > 8 MB with mock ones
tests/files/gaussian/linear_bend.out
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for large text files, it's best to gzip or lzma compress them
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thanks @rashatwi. i made a few more changes but don't have permission to push to this PR. could you check the box saying "allow edits from maintainers"? |
Looks like I cannot "allow edits from maintainers" if I'm doing the PR from an organization account Please check this |
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i see. i didn't know about this restriction for org forks. i just pushed a new 1f8e2a6 move matplotlib import into _monitor_convergence could you have a look at those changes and see if they make sense, esp. in 180990b? if so, would be great if you could change your target branch on this PR from |
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Done |
* Add the start of the Gaussian handler * Add the start of the Gaussian job * Add the start of the Gaussian custodian * Add matplotlib to requirements * Define better_scf_guess job * Correct scf cycles error handling * Add an option to check convergence as a function of iterations * Implement opt_steps error handling * Implement solute_solvent_surface error handling * Change integration grid * Update Gaussian integration grids * Generate a better geom guess at a lower LOT * Update better_guess job to be used with OPT and SCF job types * Add more error definitions * Add integral keyword to route_parameters * Remove empty spaces in route_params dict * Plot convergence only if data is available * Restart opt calc if it appears to be converging * Correct torsion error handler * Cleanups * Handle more errors * Cleanups * Correct how the integration grid is read * Correct the conversion of convergence data to floats * Correct the error of internal coords by performing opt using cart coords and disabling symmetry * Handle insufficient memory * Fix bug in reading scf parameters * Add wall time handler * Postprocess job * Add the start of the Gaussian handler * Add the start of the Gaussian job * Add the start of the Gaussian custodian * Define better_scf_guess job * Correct scf cycles error handling * Add an option to check convergence as a function of iterations * Implement opt_steps error handling * Implement solute_solvent_surface error handling * Change integration grid * Update Gaussian integration grids * Generate a better geom guess at a lower LOT * Update better_guess job to be used with OPT and SCF job types * Add more error definitions * Add integral keyword to route_parameters * Remove empty spaces in route_params dict * Plot convergence only if data is available * Restart opt calc if it appears to be converging * Correct torsion error handler * Cleanups * Handle more errors * Cleanups * Correct how the integration grid is read * Correct the conversion of convergence data to floats * Correct the error of internal coords by performing opt using cart coords and disabling symmetry * Handle insufficient memory * Fix bug in reading scf parameters * Add wall time handler * Postprocess job * Add gaussian dependencies * Add docstrings and use directory as input arg * Add terminate function to kill Gaussian job * Update Gaussian custodian version * Use directory as input * Bug fixes * Linting * Linting * Update Gaussian custodian version * Cleanups * Remove old backup_gaussian_files function * Add Gaussian handler docstrings * Update docstrings * Update docstrings * Fix typo in WallTimeErrorHandler * Add Gaussian tests * Add Gaussian test files * Deactivate better guess after running test * Remove duplicate tearDown func * Correct class name * Change rwf assertion statement * Linting * Bug fix in matching error type * Replace actual Gaussian checkpoint files with mock ones * Gzip Gaussian output files * move matplotlib import into _monitor_convergence * add type annotations to GaussianJob * Change better_guess func name in tests * Add type annotations to GaussianErrorHandler * `float` instead of `int | float` for mem * New Gaussian plugin (#325) * Change better_guess func name in tests * Add type annotations to GaussianErrorHandler * `float` instead of `int | float` for mem * ruff str format fixes, date assert refactor, rename test jobs * Fix issue with gaussian .gz files --------- Co-authored-by: Rasha <atwi.r@husky.neu.edu>
Add new job and handler modules for various Gaussian errors along with their unittests. Examples of handled errors include:
Among others