Code

Simplify Chemical System#616

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MBartkowiakSTFC merged 89 commits intoprotosISISNeutronMuon/MDANSE:protosfrom maciej/simplify-chemical-systemISISNeutronMuon/MDANSE:maciej/simplify-chemical-systemCopy head branch name to clipboardJan 30, 2025

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Commits

Commits on Nov 19, 2024

• Add trajectory methods for reading atom properties

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  6a2be13

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Commits on Nov 20, 2024

• Add method for adding a single atom to trajectory database

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• Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE into maciej/atom-database-in-trajectory

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• Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE into maciej/atom-database-in-trajectory

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Commits on Nov 21, 2024

• Make converters add standars atom database to trajectory

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• Read atom properties from trajectory

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• Make weights configurator depend on trajectory

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  26e1e44

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• Add types to the database

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  2d92969

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• Replace recursive graph walking with networkx

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  6b408e0

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• Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE into maciej/atom-database-in-trajectory

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• Merge branch 'maciej/improve-trajectory-editor' into maciej/atom-database-in-trajectory

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• Make molecule detection fault-tolerant

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Commits on Nov 22, 2024

• Remove most ChemicalEntity subclasses

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• Remove most of ChemicalEntity.py

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Commits on Nov 25, 2024

• Remove references to other chemical entities

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• Remove references to other chemical entities

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Commits on Nov 26, 2024

• Simplify configuration writing

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  cdf548a

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• Update Configuration code

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• Remove Graph.py

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  2e2942b

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• Update TrajectoryUtils

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  01b2b60

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• Correct some tests

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Commits on Nov 27, 2024

• Make converter tests pass

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  98ae0eb

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• Enable loading old trajectories

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  3b2d1fb

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• Make GUI jobs executable

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  8264962

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• Remove unused Cython code

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• Replace contiguous_coordinates.pyx with Python code

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Commits on Nov 28, 2024

• Make configuration unit tests pass

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  745799b

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• Simplify continuous coordinate calculation

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• Replace com_trajectory extension with Python code

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• Make tests runnable

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  eaff565

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• Make unittest tests pass

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  af4c1de

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• Fix problems with TrajectoryEditor

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Commits on Nov 29, 2024

• Remove mic_fast_calc from Extensions

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  92fc4e9

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• Make all tests pass

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  a4311dc

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• Rewrite SolventAccesibleSurface

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  61b60ea

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• Correct the SolventAccessibleSurface implementation

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  984c4b9

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• Clean up unneccessary files

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  2691c51

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• Remove unused cluster class

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  3f41321

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• Remove unused extension imports

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  81991a3

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Commits on Dec 1, 2024

• Correct Voronoi coordinate padding

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Commits on Dec 2, 2024

• Correct the Solvent Accessible Surface calculation

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  2aa2627

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• Add periodic boundary condition handling to solvent accessible surface

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  e54dc8d

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• Reduce the number of structure analysis tests

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  ee65d6c

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• Enable CentreOfMass trajectories with fake atoms

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Commits on Dec 3, 2024

• Remove the last Cython extension

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  cafd01a

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• Reduce the number of open and close operations when reading trajectories

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• Merge GUI changes

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  73d775b

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• Improve the separation into inter and intra in PDF

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• Explicitly close trajectory in test_converter.py

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• Add tests for centre-of-mass trajectory with artificial atoms

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Commits on Dec 4, 2024

• Delete obsolete files

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• Bring back setup.py

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Commits on Dec 11, 2024

• Add special atom property for marking dummy atoms

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  6fc1e56

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• Add dummy atom handling for centre-of-mass atoms

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Commits on Dec 12, 2024

• Merge recent changes from protos

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  eb5b51b

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• Clean up unused files

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  f9cdfd0

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• Start cleaning up atom grouping

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Commits on Jan 2, 2025

• Merge branch 'protos' into maciej/simplify-chemical-system

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  e990618

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• Remove Extensions from source code tree

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  663896f

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• Modify van Hove distinct function

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Commits on Jan 3, 2025

• Restructure DistanceHistogram

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Commits on Jan 6, 2025

• Speed up the van Hove distinct function calculation

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  fb189c9

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Commits on Jan 14, 2025

• Fix atom sorting in LAMMPS trajectories

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• Initialise Forcite positions from XTD file

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Commits on Jan 15, 2025

• Add molecule building to converters

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  085167e

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• Correct converters and atom naming

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  d1c29f0

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• Merge branch 'protos' into maciej/simplify-chemical-system

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  2fa0df1

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• Adapt the MDTraj converter to the new ChemicalSystem

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  7871d4a

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• Add bond reading to MDTraj converter

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  17ee150

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• Close trajectory explicitly in MDTraj converter tests

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  e310f72

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Commits on Jan 16, 2025

• Explicitly close a deleted trajectory file in TrajectoryView

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Commits on Jan 17, 2025

• Explicitly close the file in the MdanseTrajectory ChemicalSystem check

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• Make padded_coordinate consistent between Voronoi and SolventAccessibleSurface

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Commits on Jan 20, 2025

• Include molecule radius in artificial atom radii for COM trajectories

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  f98f33d

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• Copy bonds and molecules on a null TrajectoryEditor run

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  a7588f2

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Commits on Jan 22, 2025

• Improve contiguous configuration calculation

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Commits on Jan 23, 2025

• Correct PDB reader, add bring_to_centre to contiguous configuration

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• Add missing function parameter in RealConfiguration

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• Correct the scaling factor in StaticStructureFactor

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Commits on Jan 24, 2025

• Fix q vector generator switching in the GUI

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  b3bb2ec

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• Improve default input parameters of DistanceHistogram-based jobs

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Commits on Jan 27, 2025

• Do not run centre of mass on a single atom

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Commits on Jan 28, 2025

• Improve com_trajectory and grouping

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• Remove cell from contiguous_coordinates_box

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Commits on Jan 29, 2025

• Change a configuration test result

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  cab8301

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• Clean up centre of mass trajectory

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  2699ec4

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• Remove unused files

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  4863da7

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• Apply black

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  fde578b

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• Fix the handling of H5MD trajectories

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