Code

Descriptor calculation in python#510

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RandomDefaultUser merged 51 commits intomala-project:developmala-project/mala:developfrom RandomDefaultUser:descriptors_pythonRandomDefaultUser/mala:descriptors_pythonCopy head branch name to clipboardApr 5, 2024

+1,242-106

Commits

Commits on Feb 23, 2024

• Started working on descriptor calculation in python

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  3e9e90c

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• Reproduced LAMMPS grid (except for the bounding boxes?)

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  45e061e

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• Gaussian descriptors almost working

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  5c13b65

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Commits on Feb 26, 2024

• Working on neighborlist

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  6638994

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• Gaussian descriptors working - albeit terribly slow

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  48a39b8

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• Trying to do sort of a global neighborhood list

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  7a0dc61

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Commits on Feb 28, 2024

• Efficient implementation of Gaussian descriptors

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  8aaf480

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• Made grid dimensions, atoms and voxel Descriptor class properties

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  6be732a

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• Made interface consistent

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  137071e

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• Further optimization

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  e32d13f

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• Further optimization

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  41c8818

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• I think I optimized something

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  4116480

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• Retook one optimization

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  67ff378

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Commits on Feb 29, 2024

• Bugfix in optimized implementation

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  4161c06

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• Tried to reduce the list of all atoms further

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  7f2a623

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• Small bugfix

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  358013f

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Commits on Mar 12, 2024

• Cleaned up the code and committed to skspatial

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  3b19ef8

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Commits on Mar 13, 2024

• Started with bispectrum descriptors

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  749dfb9

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Commits on Mar 19, 2024

• Implemented Ui

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  22e544e

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Commits on Mar 20, 2024

• Implemented zi

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  ac5d3cc

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• Got bi

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• Calculation finished, just probably very very slow

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  76f64b6

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• Some fun bispectrum debugging

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  c30f3dc

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Commits on Mar 21, 2024

• compute ui working

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  21bad16

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Commits on Mar 22, 2024

• Continuing to bugfix

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  de8a6bd

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Commits on Mar 23, 2024

• Debugged some more

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  f7e341e

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• zi is working now

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Commits on Mar 28, 2024

• Bispectrum descriptors working now, but very slow

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  2cfbdac

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• Implemented some very obvious optimizations

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  24fc6c1

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Commits on Apr 2, 2024

• Another small improvement

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  9fe82a0

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• Optimized ui; the code is horrible, but fast-ish

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  b9c7d3e

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• Trying something with compute_zi, not yet finished

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Commits on Apr 3, 2024

• This compute_zi function is not yet working - but it would roughly be fast enough

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  53afa7a

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• The unvectorized version is working

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  46921d5

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• Still debugging

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• Fastest version as of yet

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  9fcdebd

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• (Cleaned) Fastest version as of yet

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  6ef0aef

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• A bit more cleaning

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Commits on Apr 4, 2024

• Started a full cleanup

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  659d4d8

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• More cleaning up

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  72cddba

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• Almost finished with cleaning up

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  9dfd88e

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• Added warning for python based calculation

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  2351fa0

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• Made python a fallback for the descriptor calculation.

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  9b269eb

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• Fixed docstrings

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  6694e6a

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• Fixed docs

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  7a47fcb

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• Added a test and adapted some others

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  a51aac4

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• Small adjustments for the documentation

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  dfe1e18

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• Corrected Typo

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  a7d9fa2

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• Added missing requirement

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  ccdd5fe

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• Added missing requirement

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• Trying a different scikit-spatial version

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