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Dev/sym opt #111

Merged
merged 26 commits into from
Jan 28, 2025
Merged

Dev/sym opt #111

merged 26 commits into from
Jan 28, 2025

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jonathan-schoeps
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A new class is added which multiply the mindless molecule by a symmetry operation to generate larger NCI complexes.
As added symmetry operations the following operations were chosen.

  • Mirror
  • Cn Rotation
  • Inversion

@jonathan-schoeps
Interface for the qm program turbomole
f6a3282 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
support for turbomole
d6c60c2 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
Merge branch 'main' into dev/tm_interface
eefcb3f 
Merge latest changes to dev branche
@jonathan-schoeps
corrected some typos
0a20340 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
structure_mod baseline
e4f79b7 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
Merge branch 'main' into dev/symmetrie_operations
44cec38 
Update the branch
@jonathan-schoeps
baseline for the symmetrie class
a1f9716 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
Implementation of the structur modification module containing Cn rota…
144e309 
…tion, mirror and inversion

Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
merged recent changes
6e2c63f 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
update to the structure_modification routine and implemented unit tests.
e5513ec 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps
removal of left over dead code snippets
7d0e5b2 
Signed-off-by: Jonathan Schöps <[email protected]>
@jonathan-schoeps jonathan-schoeps self-assigned this Jan 22, 2025
@jonathan-schoeps jonathan-schoeps added the algorithm Related to the back-end algorithm for generating the mindless molecules. label Jan 22, 2025
@jonathan-schoeps jonathan-schoeps linked an issue Jan 22, 2025 that may be closed by this pull request
TM class for TURBOMOLE interface #90
Closed
@jonathan-schoeps jonathan-schoeps removed a link to an issue Jan 22, 2025
TM class for TURBOMOLE interface #90
Closed
This was linked to issues Jan 22, 2025
Symmetry operations for NCI complexes with MindlessGen #86
Closed
Call for structure_modification container in main #88
Closed
StructureModConfig #89
Closed
Parent class (abstract!) and subclasses StrucMod for the structure modifications #91
Closed
Subclasses of StructureModModel #92
Closed
@marcelmbn
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Please update the local branch with the latest updates from main.

marcelmbn
marcelmbn reviewed Jan 22, 2025
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marcelmbn commented Jan 23, 2025 •
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Some general remarks

I'd say we should prefer following the implementation strategy discussed in this issue and its sub-issues: #86
The PR is not the place for a discussion of how (strategically) implement something but this should rather be defined in issues or discussions (https://github.com/grimme-lab/MindlessGen/discussions).

Object-oriented implementation

marcelmbn and others added 8 commits January 28, 2025 10:51
@marcelmbn
abstract structure merge; minor revisions for config
a6b61d5 
Signed-off-by: Marcel Müller <[email protected]>
@jonathan-schoeps
Fix to print the correct output of tm and remove of a redundant singl…
d5b5fc8 
…epoint calculation

Signed-off-by: Jonathan Schöps <[email protected]>
@marcelmbn
distance check for clashes and iterative distance increase if too low
f7599c8 
Signed-off-by: Marcel Müller <[email protected]>
@marcelmbn
rename some file and Class names to typical conventions
76b06ff 
Signed-off-by: Marcel Müller <[email protected]>
@marcelmbn
further variable renaming; config clean-up
2fe6b50 
Signed-off-by: Marcel Müller <[email protected]>
@marcelmbn
add CLI access for arguments and minor adaptions
4b25ca4 
Signed-off-by: Marcel Müller <[email protected]>
@marcelmbn
update default TOML file
3354eac 
Signed-off-by: Marcel Müller <[email protected]>
@marcelmbn
some renamings, better docstrings, remove useless variable copies
379b6ab 
Signed-off-by: Marcel Müller <[email protected]>
@jonathan-schoeps jonathan-schoeps merged commit e986bfc into grimme-lab:main Jan 28, 2025
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@jonathan-schoeps jonathan-schoeps deleted the dev/sym_opt branch January 28, 2025 16:06
@jonathan-schoeps jonathan-schoeps mentioned this pull request Jan 28, 2025
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@marcelmbn marcelmbn marcelmbn approved these changes

@lmseidler lmseidler Awaiting requested review from lmseidler lmseidler is a code owner

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