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QTAIM Surface Algorithm #56
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Commits on Sep 5, 2022
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Commits on Sep 6, 2022
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Commits on Jan 4, 2023
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- Added gradient path vectorized - Added beta-spheres
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Commits on Jan 25, 2023
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- Write RK4(5) ODE solver - Vectorize over radial shells
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Commits on Feb 2, 2023
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Commits on Feb 8, 2023
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Commits on Feb 9, 2023
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Commits on Feb 16, 2023
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Commits on Feb 20, 2023
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Commits on Feb 22, 2023
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- Added a maximum iteration to ODE solver - Added check for NNA
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Commits on Mar 13, 2023
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Update how atom grid surface is calculated
- Still needs refactoring
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Commits on Mar 17, 2023
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Commits on Apr 11, 2023
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Add multiple intersection finding
- Finding the intersections isn't added yet
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Add another method of finding IAS
- Took from Keith's thesis CH4, faster than solving for an entire interval at a time
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- Beta-spheres to the Surface object - Spherical t-design to the grid objects
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Commits on Apr 12, 2023
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For refinement, added check for OAS pts
Points that are IAS should really be on the isosurface
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Commits on Apr 14, 2023
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Change OAS root solving is done
Complicated molecules weren't converging, this is due to how termination is set in scipy.optimize.root. Since this root-solving is independent on its coordinates, the norm convergence is set to l_inf.
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Ali-Tehrani committed
Apr 14, 2023 Configuration menu - View commit details
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Commits on Apr 15, 2023
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Reduce printing when solving for IAs
Ali-Tehrani committedApr 15, 2023 Configuration menu - View commit details
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Commits on Apr 16, 2023
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Add second attempt to solving OAS points
- Sometimes the root-solver doesn't converge. Added a individual solver for each point that didnt't converge
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Commits on Apr 20, 2023
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Change root-solving to Newton-Ralpson
Hard to get correct solution of scipy.optimize.root. This requires writing own Newton-Ralpson code to achieve this.
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Add a check for IAS points that should be OAS
If the points along IAS have density values less than the isosurface value then it corrects it by assigning it be part of the isosurface instead.
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Fix obj func in solving root eqn second time
Ali-Tehrani committedApr 20, 2023 Configuration menu - View commit details
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Commits on Apr 26, 2023
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Raise error if NNA is found or BCP/RCP converged
Makes it easier to do error handling for edge cases
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Add ability to surface to handle subset of atoms
This increases performance because not all atoms need to be re-computed.
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Commits on Apr 27, 2023
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Commits on May 1, 2023
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Add new method of solving for root of isosurface
- Moves along the ray taking small step-size. - Purpose:gets the first root when there is multiple roots along the ray.
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Update the qtaim surface algorithm
- Update to fit the new solving for OAS - Added new parameters to control the radial grids, since they control the decision on a ray to be on OAS or IAS - Update docs
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Commits on Jun 9, 2023
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Update parameters for beta-sphere
Ali-Tehrani committedJun 9, 2023 Configuration menu - View commit details
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- Replaced by qtaim.py and qtaim_depreciated.py
Ali-Tehrani committedJun 9, 2023 Configuration menu - View commit details
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Commits on Jun 24, 2023
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Ali-Tehrani committed
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Fix finding nna in beta-sphere search with hessian
Ali-Tehrani committedJun 24, 2023 Configuration menu - View commit details
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Add rotation check for beta-spheres
- Makes sure the beta-sphere is correct.
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- Lots of molecules actually do intersect the basin more than three times
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Add step-size radial grid to differ per atom
- Increases time efficiency
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Commits on Sep 14, 2023
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Add option to include optional degree
- Can create any angular degree
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Commits on Sep 25, 2023
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Commits on Sep 26, 2023
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Add no refinement if not enough points on OAS
Ali-Tehrani committedSep 26, 2023 Configuration menu - View commit details
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Decrease beta-sphere when NNA are found
- The NNA was incredibly close and so the beta-sphere must have been decreased
Ali-Tehrani committedSep 26, 2023 Configuration menu - View commit details
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Add option for having minimal radial point to API
Ali-Tehrani committedSep 26, 2023 Configuration menu - View commit details
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Commits on Sep 29, 2023
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Fix bug in getting IAS and surface points
- np.unique doesn't preserve order
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Commits on Oct 18, 2023
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Commits on Oct 23, 2023
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Fix density issue when using beta-spheres
- Sometimes the beta-sphere is so large, that there are points on the sphere whose density values are less than isosurface value, these points should b e classified as oas or else it will cause an IndexError
Ali-Tehrani committedOct 23, 2023 Configuration menu - View commit details
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Commits on Nov 7, 2023
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- only for surface atoms, because it doesn't work with negative indices
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Ali-Tehrani committed
Nov 7, 2023 Configuration menu - View commit details
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Commits on Nov 22, 2023
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Commits on Feb 20, 2024
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Change correct type for later numpy
Ali-Tehrani committedFeb 20, 2024 Configuration menu - View commit details
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Ali-Tehrani committed
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Commits on May 10, 2024
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Commits on May 23, 2024
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Add to utils hirshfeld surface finder
- Need this for refinement within Surface class
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