Fix random number generation by removing legacy random number generation #78
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Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
jonathan-schoeps
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Nov 13, 2024
marcelmbn
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Nov 18, 2024
* Update Docs (#72) * update docs, co-workers, pyproject.toml, remove typos Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * update CHANGELOG, make case more consistent Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * update mindlessgen.toml Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * align defaults Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * update reference default value Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * update tests Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * correct inconsistent boolean Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> --------- Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * Fix random number generation by removing legacy random number generation (#78) * fix random number generation by incorporating default_rng Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * update CHANGELOG.md Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> --------- Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * Remove deprecated tests that are not strictly true (#79) * remove deprecated tests Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * remove random numpy seed as it's pointless now Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> --------- Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * A fixed molecular charge for the molecule generation. (#73) * A new function to set a fixed charge value Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * latest changes to the fixed charge method Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Fixed charge and element composition works test have to be added Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * More modular fixed charge routine Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * complete fixed charge routine Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Removed an unnessesary import Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * more convenient function name Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Worked in the suggested changes Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Added a changelog entry Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Changes a bug with an array type Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * removed left over print statements Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Implemented requested changes Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Added a new test to raise a ValueError Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> --------- Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * `atlist` to `ati` and back conversion (#81) * implement atlist to ati conversion Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * add conversion test Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> --------- Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * Bug fix were uhf was always 0 if a fixed charge were given (#80) * bug fix were uhf was always 0 if a fixed charge were given Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * updated a test for the right uhf Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * get rid of redundant code within set_random_charge Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * using atlist as a variable in misscellaneous Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> --------- Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * adapt CODEOWNERS to commit history (#82) Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> * The `.UHF` file is now written if the molecule has a uhf larger than 0 (#74) * The .UHF file is now written if the molecule has a uhf larger than 0 Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Writes the .CHRG file if the charge is larger than 0 Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * charge and uhf can be None Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * Negative charge is now written aswell Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> --------- Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> * update CHANGELOG Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> --------- Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de> Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de> Co-authored-by: Jonathan Schöps <106986430+jonathan-schoeps@users.noreply.github.com>
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np.random.randint(...statements withnumatoms_all = rng.integers(...based on initialization of a default random number generator fromnumpy:np.random.default_rng().