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Simplify Chemical System #616

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Simplify Chemical System #616

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6a2be13
Add trajectory methods for reading atom properties
MBartkowiakSTFC Nov 19, 2024
7a246fa
Add method for adding a single atom to trajectory database
MBartkowiakSTFC Nov 20, 2024
928ebc4
Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in…
MBartkowiakSTFC Nov 20, 2024
e0a1796
Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in…
MBartkowiakSTFC Nov 20, 2024
d047c7c
Make converters add standars atom database to trajectory
MBartkowiakSTFC Nov 21, 2024
56cb17a
Read atom properties from trajectory
MBartkowiakSTFC Nov 21, 2024
26e1e44
Make weights configurator depend on trajectory
MBartkowiakSTFC Nov 21, 2024
2d92969
Add types to the database
MBartkowiakSTFC Nov 21, 2024
6b408e0
Replace recursive graph walking with networkx
MBartkowiakSTFC Nov 21, 2024
31c8c5b
Merge branch 'protos' of https://github.com/ISISNeutronMuon/MDANSE in…
MBartkowiakSTFC Nov 21, 2024
088f310
Merge branch 'maciej/improve-trajectory-editor' into maciej/atom-data…
MBartkowiakSTFC Nov 21, 2024
8ab32e1
Make molecule detection fault-tolerant
MBartkowiakSTFC Nov 21, 2024
f18a9e7
Remove most ChemicalEntity subclasses
MBartkowiakSTFC Nov 22, 2024
e9b5067
Remove most of ChemicalEntity.py
MBartkowiakSTFC Nov 22, 2024
259ddae
Remove references to other chemical entities
MBartkowiakSTFC Nov 25, 2024
f439ae6
Remove references to other chemical entities
MBartkowiakSTFC Nov 25, 2024
cdf548a
Simplify configuration writing
MBartkowiakSTFC Nov 26, 2024
8b56b36
Update Configuration code
MBartkowiakSTFC Nov 26, 2024
2e2942b
Remove Graph.py
MBartkowiakSTFC Nov 26, 2024
01b2b60
Update TrajectoryUtils
MBartkowiakSTFC Nov 26, 2024
7586dc8
Correct some tests
MBartkowiakSTFC Nov 26, 2024
98ae0eb
Make converter tests pass
MBartkowiakSTFC Nov 27, 2024
3b2d1fb
Enable loading old trajectories
MBartkowiakSTFC Nov 27, 2024
8264962
Make GUI jobs executable
MBartkowiakSTFC Nov 27, 2024
5a373a5
Remove unused Cython code
MBartkowiakSTFC Nov 27, 2024
840001e
Replace contiguous_coordinates.pyx with Python code
MBartkowiakSTFC Nov 27, 2024
745799b
Make configuration unit tests pass
MBartkowiakSTFC Nov 28, 2024
bad4680
Simplify continuous coordinate calculation
MBartkowiakSTFC Nov 28, 2024
17a69b6
Replace com_trajectory extension with Python code
MBartkowiakSTFC Nov 28, 2024
eaff565
Make tests runnable
MBartkowiakSTFC Nov 28, 2024
af4c1de
Make unittest tests pass
MBartkowiakSTFC Nov 28, 2024
e5bb81e
Fix problems with TrajectoryEditor
MBartkowiakSTFC Nov 28, 2024
92fc4e9
Remove mic_fast_calc from Extensions
MBartkowiakSTFC Nov 29, 2024
a4311dc
Make all tests pass
MBartkowiakSTFC Nov 29, 2024
61b60ea
Rewrite SolventAccesibleSurface
MBartkowiakSTFC Nov 29, 2024
984c4b9
Correct the SolventAccessibleSurface implementation
MBartkowiakSTFC Nov 29, 2024
2691c51
Clean up unneccessary files
MBartkowiakSTFC Nov 29, 2024
3f41321
Remove unused cluster class
MBartkowiakSTFC Nov 29, 2024
81991a3
Remove unused extension imports
MBartkowiakSTFC Nov 29, 2024
3d79122
Correct Voronoi coordinate padding
MBartkowiakSTFC Dec 1, 2024
2aa2627
Correct the Solvent Accessible Surface calculation
MBartkowiakSTFC Dec 2, 2024
e54dc8d
Add periodic boundary condition handling to solvent accessible surface
MBartkowiakSTFC Dec 2, 2024
ee65d6c
Reduce the number of structure analysis tests
MBartkowiakSTFC Dec 2, 2024
b134f90
Enable CentreOfMass trajectories with fake atoms
MBartkowiakSTFC Dec 2, 2024
cafd01a
Remove the last Cython extension
MBartkowiakSTFC Dec 3, 2024
9a42ec3
Reduce the number of open and close operations when reading trajectories
MBartkowiakSTFC Dec 3, 2024
73d775b
Merge GUI changes
MBartkowiakSTFC Dec 3, 2024
e716cd9
Improve the separation into inter and intra in PDF
MBartkowiakSTFC Dec 3, 2024
bec58c6
Explicitly close trajectory in test_converter.py
MBartkowiakSTFC Dec 3, 2024
2c2b563
Add tests for centre-of-mass trajectory with artificial atoms
MBartkowiakSTFC Dec 3, 2024
556c956
Delete obsolete files
MBartkowiakSTFC Dec 4, 2024
5e6efe8
Bring back setup.py
MBartkowiakSTFC Dec 4, 2024
6fc1e56
Add special atom property for marking dummy atoms
MBartkowiakSTFC Dec 11, 2024
2914526
Add dummy atom handling for centre-of-mass atoms
MBartkowiakSTFC Dec 11, 2024
eb5b51b
Merge recent changes from protos
MBartkowiakSTFC Dec 12, 2024
f9cdfd0
Clean up unused files
MBartkowiakSTFC Dec 12, 2024
40cfe32
Start cleaning up atom grouping
MBartkowiakSTFC Dec 12, 2024
e990618
Merge branch 'protos' into maciej/simplify-chemical-system
MBartkowiakSTFC Jan 2, 2025
663896f
Remove Extensions from source code tree
MBartkowiakSTFC Jan 2, 2025
837d22d
Modify van Hove distinct function
MBartkowiakSTFC Jan 2, 2025
d500f10
Restructure DistanceHistogram
MBartkowiakSTFC Jan 3, 2025
fb189c9
Speed up the van Hove distinct function calculation
MBartkowiakSTFC Jan 6, 2025
38866ea
Fix atom sorting in LAMMPS trajectories
MBartkowiakSTFC Jan 14, 2025
fd82911
Initialise Forcite positions from XTD file
MBartkowiakSTFC Jan 14, 2025
085167e
Add molecule building to converters
MBartkowiakSTFC Jan 15, 2025
d1c29f0
Correct converters and atom naming
MBartkowiakSTFC Jan 15, 2025
2fa0df1
Merge branch 'protos' into maciej/simplify-chemical-system
MBartkowiakSTFC Jan 15, 2025
7871d4a
Adapt the MDTraj converter to the new ChemicalSystem
MBartkowiakSTFC Jan 15, 2025
17ee150
Add bond reading to MDTraj converter
MBartkowiakSTFC Jan 15, 2025
e310f72
Close trajectory explicitly in MDTraj converter tests
MBartkowiakSTFC Jan 15, 2025
b98bfda
Explicitly close a deleted trajectory file in TrajectoryView
MBartkowiakSTFC Jan 16, 2025
25e2e16
Explicitly close the file in the MdanseTrajectory ChemicalSystem check
MBartkowiakSTFC Jan 17, 2025
5210305
Make padded_coordinate consistent between Voronoi and SolventAccessib…
MBartkowiakSTFC Jan 17, 2025
f98f33d
Include molecule radius in artificial atom radii for COM trajectories
MBartkowiakSTFC Jan 20, 2025
a7588f2
Copy bonds and molecules on a null TrajectoryEditor run
MBartkowiakSTFC Jan 20, 2025
6b90fa9
Improve contiguous configuration calculation
MBartkowiakSTFC Jan 22, 2025
3da6b5e
Correct PDB reader, add bring_to_centre to contiguous configuration
MBartkowiakSTFC Jan 23, 2025
dd0f904
Add missing function parameter in RealConfiguration
MBartkowiakSTFC Jan 23, 2025
23c3082
Correct the scaling factor in StaticStructureFactor
MBartkowiakSTFC Jan 23, 2025
b3bb2ec
Fix q vector generator switching in the GUI
MBartkowiakSTFC Jan 24, 2025
3407469
Improve default input parameters of DistanceHistogram-based jobs
MBartkowiakSTFC Jan 24, 2025
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6 changes: 0 additions & 6 deletions MDANSE/Extensions/.gitignore
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162 changes: 0 additions & 162 deletions MDANSE/Extensions/atoms_in_shell.pyx
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206 changes: 0 additions & 206 deletions MDANSE/Extensions/com_trajectory.pyx
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