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Extend model system#58

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ndaelman-hu wants to merge 31 commits intodevelopnomad-coe/nomad-simulations:developfrom extend_model_systemnomad-coe/nomad-simulations:extend_model_systemCopy head branch name to clipboard

+759-88

Commits

Commits on Apr 18, 2024

• - Add first implementation of bond length calculation + tests

  Show description for 92785b9
  

  ndaelman

  committed
  92785b9

Commits on Apr 19, 2024

• Fix typos

  

  ndaelman

  committed
  e60bceb

• Fix typos

  

  ndaelman

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  6ddc77c

• Improve pbc default system\

  

  ndaelman

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  a1cd476

Commits on Apr 23, 2024

• - Accomodate schema for hosting interatomic distances

  Show description for 68b5d32
  

  ndaelman

  committed
  68b5d32

• - Add angles

  Show description for 8e3e859
  

  ndaelman

  committed
  8e3e859

Commits on Apr 24, 2024

• - Fix shape issue with elementals

  Show description for c05e46e
  

  Nathan Daelman

  committed
  c05e46e

Commits on Apr 26, 2024

• - Restructure functionalities into a chain of factory classes

  Show description for 12246f1
  

  ndaelman

  committed
  12246f1

• Fix some mistakes

  

  Nathan Daelman

  committed
  e63c987

• - Work out distance and angle values tests for ethane

  Show description for 479725a
  

  ndaelman

  committed
  479725a

Commits on Apr 28, 2024

• Add test for DistributionFactory

  

  ndaelman

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  d0506a3

• - Add tests for DistributionHistogram

  Show description for 81b3ece
  

  ndaelman

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  81b3ece

• Improve analyze_geometry check

  

  ndaelman

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  897ccb6

Commits on May 13, 2024

• Apply reviewer feedback

  

  ndaelman

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  5440b4d

• Rename GeometryDistribution.elements to GeometryDistribution.atom_labels as per reviewer request

  

  ndaelman

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  fd1bff9

• - Split out GeometryDistribution in to subcases (resolving reviewer feedback)

  Show description for 1539c15
  

  ndaelman

  committed
  1539c15

• Correct typing (mypy)

  

  ndaelman

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  333f15c

Commits on May 17, 2024

• - Merge branch 'develop' into extend_model_system

  Show description for 45e12aa
  

  ndaelman

  committed
  45e12aa

• Fix indentation error AtomicCell.to_ase_atoms()

  

  ndaelman

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  e8f59f8

• Move bond_list from Cell ro AtomicCell upon reviewer request

  

  ndaelman

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  208c2ba

• Reapply @check_attributes to to_ase_atoms

  

  ndaelman

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  a398857

• - Remove positions and velocities from AtomicCell, in favor of those in Cell.

  Show description for 7265b53
  

  ndaelman

  committed
  7265b53

• Add test for GeometryDistribution (instantiation and normalization)

  

  ndaelman

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  4333a53

• - Add test case to test_distribution_histogram

  Show description for 2b9c287
  

  ndaelman

  committed
  2b9c287

• Change GeometricDistribution units for angles from degrees to radian

  

  ndaelman

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  a3ac6a3

• - Add documentation

  Show description for 9023837
  

  ndaelman

  committed
  9023837

• Fix mypy typing nameclash (gosh, mypy sucks)

  

  ndaelman

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  4da9060

Commits on May 23, 2024

• - Build in non-stored default for bins in archive storage

  Show description for 6a6305a
  ndaelman

  committed
  6a6305a

Commits on May 27, 2024

• - Remove check_attrributes

  Show description for 4c2bf8c
  ndaelman

  committed
  4c2bf8c

• - add bin units in pipeline classes

  Show description for b498bd7
  ndaelman

  committed
  b498bd7

• - Fix mypy errors

  Show description for 4e92474
  ndaelman

  committed
  4e92474