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A fixed molecular charge for the molecule generation. #73

Merged
merged 17 commits into from
Nov 15, 2024
Merged

A fixed molecular charge for the molecule generation. #73

merged 17 commits into from
Nov 15, 2024

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jonathan-schoeps
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@jonathan-schoeps jonathan-schoeps commented Nov 11, 2024 •
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According to issue #68 the following change was made.

  • Add a function to set a charge for the molecule generation but ensure that the molecule is closed shell. This is done by adding or removing an atom, which depends on the overall configuration.

  • This function is controllable via the .toml file and the CLI.

  • The function is the last step within the atom list generation.

@jonathan-schoeps
A new function to set a fixed charge value
743a91b 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
latest changes to the fixed charge method
156efe4 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
Merge branch 'main' into dev/fixed_charge
1c2b900
@jonathan-schoeps
Fixed charge and element composition works test have to be added
c73476b 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
More modular fixed charge routine
9a21d23 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
complete fixed charge routine
078109f 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
lates pull from upstream
92bf0e5 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
Removed an unnessesary import
3627e3b 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
more convenient function name
d67671e 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@marcelmbn marcelmbn linked an issue Nov 12, 2024 that may be closed by this pull request
Fixed charge for molecule generation #68
Closed
@marcelmbn marcelmbn added the enhancement New feature or request label Nov 12, 2024
@marcelmbn marcelmbn added this to the v1.0.0 milestone Nov 12, 2024
marcelmbn
marcelmbn requested changes Nov 12, 2024
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@jonathan-schoeps
Worked in the suggested changes
e7679d7 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
Merge branch 'main' into dev/fixed_charge
0506b64
@jonathan-schoeps
Added a changelog entry
9c6903b 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
Changes a bug with an array type
d8be3d0 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
removed left over print statements
2268553 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@jonathan-schoeps
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One unit test is failing sometimes when the number of metals within the atom list is larger than 3.

@marcelmbn
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One unit test is failing sometimes when the number of metals within the atom list is larger than 3.

Do you understand why? There might be a randomness involved, which we don't catch. I observed a similar thing today in the morning.

marcelmbn
marcelmbn requested changes Nov 14, 2024
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marcelmbn
marcelmbn requested changes Nov 15, 2024
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@jonathan-schoeps
Added a new test to raise a ValueError
ccb96c7 
Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@marcelmbn marcelmbn self-requested a review November 15, 2024 14:03
@jonathan-schoeps jonathan-schoeps merged commit 82aa3f5 into grimme-lab:main Nov 15, 2024
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@jonathan-schoeps jonathan-schoeps deleted the dev/fixed_charge branch November 15, 2024 14:56
marcelmbn added a commit that referenced this pull request Nov 18, 2024
@marcelmbn @jonathan-schoeps
Merge latest mindlessgen features into gp3_ipea (#84)
af67c88 
* 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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@marcelmbn marcelmbn marcelmbn approved these changes

@thfroitzheim thfroitzheim Awaiting requested review from thfroitzheim

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Fixed charge for molecule generation
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@jonathan-schoeps @marcelmbn