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New Gaussian job and handlers #328
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8308bdf
Add the start of the Gaussian handler
rashatwi 7a23512
Add the start of the Gaussian job
rashatwi 774d377
Add the start of the Gaussian custodian
rashatwi 6a36c48
Add matplotlib to requirements
rashatwi 3d380c4
Define better_scf_guess job
rashatwi db25860
Correct scf cycles error handling
rashatwi 83755ba
Add an option to check convergence as a function of iterations
rashatwi 81da0c0
Implement opt_steps error handling
rashatwi 9d9c7e9
Implement solute_solvent_surface error handling
rashatwi f12d40e
Change integration grid
rashatwi 7df3b8c
Update Gaussian integration grids
rashatwi 7cd6617
Generate a better geom guess at a lower LOT
rashatwi b3e4440
Update better_guess job to be used with OPT and SCF job types
rashatwi 9d69ef3
Add more error definitions
rashatwi 3dd43bf
Add integral keyword to route_parameters
rashatwi 19fb6d0
Remove empty spaces in route_params dict
rashatwi 20ff9bc
Plot convergence only if data is available
rashatwi 6e6214e
Restart opt calc if it appears to be converging
rashatwi d8c690a
Correct torsion error handler
rashatwi 91d26c6
Cleanups
rashatwi e9d9638
Handle more errors
rashatwi 59210cd
Cleanups
rashatwi 47347c0
Correct how the integration grid is read
rashatwi f8396e5
Correct the conversion of convergence data to floats
rashatwi 0826ba5
Correct the error of internal coords by performing opt using cart coo…
rashatwi ba6e3d7
Handle insufficient memory
rashatwi 10c0be4
Fix bug in reading scf parameters
rashatwi 1c33bfa
Add wall time handler
rashatwi a3ef501
Postprocess job
rashatwi 9c0dcd1
Add the start of the Gaussian handler
rashatwi d778b99
Add the start of the Gaussian job
rashatwi 9a6668a
Add the start of the Gaussian custodian
rashatwi 054c17e
Define better_scf_guess job
rashatwi f842f87
Correct scf cycles error handling
rashatwi f3e89c0
Add an option to check convergence as a function of iterations
rashatwi 3fd4820
Implement opt_steps error handling
rashatwi c3abf4d
Implement solute_solvent_surface error handling
rashatwi 42ba6c4
Change integration grid
rashatwi 47e9878
Update Gaussian integration grids
rashatwi 0a8e8e7
Generate a better geom guess at a lower LOT
rashatwi 9113286
Update better_guess job to be used with OPT and SCF job types
rashatwi 3cd9d00
Add more error definitions
rashatwi 5e01a40
Add integral keyword to route_parameters
rashatwi 685adff
Remove empty spaces in route_params dict
rashatwi 3f3e0f2
Plot convergence only if data is available
rashatwi 0b81498
Restart opt calc if it appears to be converging
rashatwi cd7d0dc
Correct torsion error handler
rashatwi 081ac1e
Cleanups
rashatwi f4539d9
Handle more errors
rashatwi 178af9d
Cleanups
rashatwi c84f8d2
Correct how the integration grid is read
rashatwi 672867a
Correct the conversion of convergence data to floats
rashatwi 345a641
Correct the error of internal coords by performing opt using cart coo…
rashatwi 2e1442f
Handle insufficient memory
rashatwi 762e12f
Fix bug in reading scf parameters
rashatwi 545dbf5
Add wall time handler
rashatwi f3bbc83
Postprocess job
rashatwi 3a2bb31
Add gaussian dependencies
rashatwi b226eaa
Add docstrings and use directory as input arg
rashatwi cb9be17
Add terminate function to kill Gaussian job
rashatwi 59b8816
Update Gaussian custodian version
rashatwi e6e40de
Use directory as input
rashatwi 5174249
Bug fixes
rashatwi 152eb5b
Linting
rashatwi 65873a6
Linting
rashatwi 37fa11f
Update Gaussian custodian version
rashatwi b59ad4d
Cleanups
rashatwi bdf7ec5
Remove old backup_gaussian_files function
rashatwi 8c32c20
Add Gaussian handler docstrings
rashatwi 7d4e096
Update docstrings
rashatwi 39f6879
Update docstrings
rashatwi aedda5a
Fix typo in WallTimeErrorHandler
rashatwi 2f08c8b
Add Gaussian tests
rashatwi 104dbba
Add Gaussian test files
rashatwi 081852e
Deactivate better guess after running test
rashatwi 2da62df
Deactivate better guess after running test
rashatwi c660c03
Remove duplicate tearDown func
rashatwi a86bdd7
Correct class name
rashatwi 282f5ee
Change rwf assertion statement
rashatwi b23ac85
Linting
rashatwi c6b31f9
Bug fix in matching error type
rashatwi 07ddbcd
Replace actual Gaussian checkpoint files with mock ones
rashatwi 5f3b204
Gzip Gaussian output files
rashatwi 1f8e2a6
move matplotlib import into _monitor_convergence
janosh 180990b
add type annotations to GaussianJob
janosh a8e6d95
Change better_guess func name in tests
rashatwi 6ba9a40
Add type annotations to GaussianErrorHandler
rashatwi b64c436
`float` instead of `int | float` for mem
rashatwi c3dcf12
New Gaussian plugin (#325)
rashatwi 851512c
ruff str format fixes, date assert refactor, rename test jobs
janosh f469ce1
Fix issue with gaussian .gz files
rashatwi 62493af
Merge branch 'master' into pr/rashatwi/331
janosh 67c79dd
Merge branch 'gaussian' into pr/rashatwi/331
janosh File filter
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| """ | ||
| This package implements various Gaussian Jobs and Error Handlers. | ||
| """ | ||
|
|
||
| __author__ = "Rasha Atwi" | ||
| __version__ = "0.1" | ||
| __maintainer__ = "Rasha Atwi" | ||
| __email__ = "rasha.atwi@stonybrook.edu" | ||
| __status__ = "Alpha" | ||
| __date__ = "5/13/21" | ||
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Condense the multi-line docstring into a single line to adhere to Python best practices.
Committable suggestion