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QTAIM Surface Algorithm #56

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QTAIM Surface Algorithm #56

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Commits on Sep 5, 2022

  1. Add qtaim voronoi and line search

    @Ali-Tehrani
    Ali-Tehrani committed Sep 5, 2022
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  2. Add tests for qtaim

    @Ali-Tehrani
    Ali-Tehrani committed Sep 5, 2022
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Commits on Sep 6, 2022

  1. Add documentation to the qtaim algorithms

    @Ali-Tehrani
    Ali-Tehrani committed Sep 6, 2022
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Commits on Jan 4, 2023

  1. Move yu-trinkle to seperate file

    @Ali-Tehrani
    Ali-Tehrani committed Jan 4, 2023
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  2. Update qtaim algorithm 

    - Added gradient path vectorized
- Added beta-spheres
    @Ali-Tehrani
    Ali-Tehrani committed Jan 4, 2023
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Commits on Jan 25, 2023

  1. Update QTAIM algorithm 

    - Write RK4(5) ODE solver
- Vectorize over radial shells
    @Ali-Tehrani
    Ali-Tehrani committed Jan 25, 2023
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Commits on Feb 2, 2023

  1. Add vectorization algorithm

    @Ali-Tehrani
    Ali-Tehrani committed Feb 2, 2023
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Commits on Feb 8, 2023

  1. Add vectorized version of qtaim algorithm

    @Ali-Tehrani
    Ali-Tehrani committed Feb 8, 2023
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Commits on Feb 9, 2023

  1. Seperate parts of algorithm into diff files

    @Ali-Tehrani
    Ali-Tehrani committed Feb 9, 2023
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Commits on Feb 16, 2023

  1. Add ode solver as arguments

    @Ali-Tehrani
    Ali-Tehrani committed Feb 16, 2023
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Commits on Feb 20, 2023

  1. Add saving isosurface value to surface object

    @Ali-Tehrani
    Ali-Tehrani committed Feb 20, 2023
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  2. Add automatic bounds for solving isosurface

    @Ali-Tehrani
    Ali-Tehrani committed Feb 20, 2023
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  3. Update tests for qtaim

    @Ali-Tehrani
    Ali-Tehrani committed Feb 20, 2023
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Commits on Feb 22, 2023

  1. Add error if non-nuclear attractor was found

    @Ali-Tehrani
    Ali-Tehrani committed Feb 22, 2023
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  2. Add stop for NNA 

    - Added a maximum iteration to ODE solver
- Added check for NNA
    @Ali-Tehrani
    Ali-Tehrani committed Feb 22, 2023
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  3. Update beta-sphere determination ODE parameters

    @Ali-Tehrani
    Ali-Tehrani committed Feb 22, 2023
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  4. Remove print statements

    @Ali-Tehrani
    Ali-Tehrani committed Feb 22, 2023
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  5. Update save in surface

    @Ali-Tehrani
    Ali-Tehrani committed Feb 22, 2023
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Commits on Mar 13, 2023

  1. Update how atom grid surface is calculated 

    - Still needs refactoring
    @Ali-Tehrani
    Ali-Tehrani committed Mar 13, 2023
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Commits on Mar 17, 2023

  1. Add finding NNA during beta-spheres

    @Ali-Tehrani
    Ali-Tehrani committed Mar 17, 2023
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  2. Add option to include extra points on surface

    @Ali-Tehrani
    Ali-Tehrani committed Mar 17, 2023
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  3. Add checking for NNA during ode solving

    @Ali-Tehrani
    Ali-Tehrani committed Mar 17, 2023
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  4. Add automatic NNA checking

    @Ali-Tehrani
    Ali-Tehrani committed Mar 17, 2023
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Commits on Apr 11, 2023

  1. Add multiple intersection finding 

    - Finding the intersections isn't added yet
    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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  2. Add another method of finding IAS 

    - Took from Keith's thesis CH4, faster than solving for an
entire interval at a time
    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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  3. Add multiple changes 

    - Beta-spheres to the Surface object
- Spherical t-design to the grid objects
    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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  4. Add beta-spheres to surface object

    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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  5. Add refinement between IAS and OAS to surface

    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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  6. Make OAS root solving faster

    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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  7. Update radial grid parameters

    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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  8. Add finding NNA to utils

    @Ali-Tehrani
    Ali-Tehrani committed Apr 11, 2023
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Commits on Apr 12, 2023

  1. For refinement, added check for OAS pts 

    Points that are IAS should really be on the isosurface
    @Ali-Tehrani
    Ali-Tehrani committed Apr 12, 2023
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  2. Update parameters in qtaim algorithm

    @Ali-Tehrani
    Ali-Tehrani committed Apr 12, 2023
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  3. Update docs in utils

    @Ali-Tehrani
    Ali-Tehrani committed Apr 12, 2023
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Commits on Apr 14, 2023

  1. 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.
    @Ali-Tehrani
    Ali-Tehrani committed Apr 14, 2023
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  2. Update angular

    Ali-Tehrani committed Apr 14, 2023
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Commits on Apr 15, 2023

  1. Update angular grid degree for NNA

    @Ali-Tehrani
    Ali-Tehrani committed Apr 15, 2023
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  2. Update solving root eqn twice if failed for OAS

    @Ali-Tehrani
    Ali-Tehrani committed Apr 15, 2023
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  3. Add a very small beta-sphere in case radial grid 

    Is very big
    @Ali-Tehrani
    Ali-Tehrani committed Apr 15, 2023
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  4. Reduce printing when solving for IAs

    Ali-Tehrani committed Apr 15, 2023
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Commits on Apr 16, 2023

  1. 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
    @Ali-Tehrani
    Ali-Tehrani committed Apr 16, 2023
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Commits on Apr 20, 2023

  1. 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.
    @Ali-Tehrani
    Ali-Tehrani committed Apr 20, 2023
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  2. Update bounds for refining the edges along IAS&OAS

    @Ali-Tehrani
    Ali-Tehrani committed Apr 20, 2023
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  3. 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.
    @Ali-Tehrani
    Ali-Tehrani committed Apr 20, 2023
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  4. Fix obj func in solving root eqn second time

    Ali-Tehrani committed Apr 20, 2023
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Commits on Apr 26, 2023

  1. Raise error if NNA is found or BCP/RCP converged 

    Makes it easier to do error handling for edge cases
    @Ali-Tehrani
    Ali-Tehrani committed Apr 26, 2023
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  2. Add ability to surface to handle subset of atoms 

    This increases performance because not all atoms need to be
re-computed.
    @Ali-Tehrani
    Ali-Tehrani committed Apr 26, 2023
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  3. Vectorize refinement of atoms 

    Increaes performance
    @Ali-Tehrani
    Ali-Tehrani committed Apr 26, 2023
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  4. Add option to check for nna

    @Ali-Tehrani
    Ali-Tehrani committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. Rename files around

    @Ali-Tehrani
    Ali-Tehrani committed Apr 27, 2023
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Commits on May 1, 2023

  1. Rename test file

    @Ali-Tehrani
    Ali-Tehrani committed May 1, 2023
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  2. Add header and update parameters to ode.py

    @Ali-Tehrani
    Ali-Tehrani committed May 1, 2023
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  3. 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.
    @Ali-Tehrani
    Ali-Tehrani committed May 1, 2023
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  4. 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
    @Ali-Tehrani
    Ali-Tehrani committed May 1, 2023
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  5. Update tests for the qtaim surface algorithm

    @Ali-Tehrani
    Ali-Tehrani committed May 1, 2023
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  6. Fix how BCP and RCP are found when backtracing

    @Ali-Tehrani
    Ali-Tehrani committed May 1, 2023
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Commits on Jun 9, 2023

  1. Update parameters for beta-sphere

    Ali-Tehrani committed Jun 9, 2023
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  2. Delete qtaim_gpu.py 

    - Replaced by qtaim.py and qtaim_depreciated.py
    Ali-Tehrani committed Jun 9, 2023
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Commits on Jun 24, 2023

  1. Fix how BCP and RCP are found

    Ali-Tehrani committed Jun 24, 2023
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  2. Fix finding nna in beta-sphere search with hessian

    Ali-Tehrani committed Jun 24, 2023
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  3. Update test

    @Ali-Tehrani
    Ali-Tehrani committed Jun 24, 2023
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  4. Add rotation check for beta-spheres 

    - Makes sure the beta-sphere is correct.
    @Ali-Tehrani
    Ali-Tehrani committed Jun 24, 2023
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  5. Fix when to check for NNA

    @Ali-Tehrani
    Ali-Tehrani committed Jun 24, 2023
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  6. Increase accuracy of basin finding in beta-sphere

    @Ali-Tehrani
    Ali-Tehrani committed Jun 24, 2023
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  7. Change raise error to warning 

    - Lots of molecules actually do intersect the basin
more than three times
    @Ali-Tehrani
    Ali-Tehrani committed Jun 24, 2023
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  8. Add step-size radial grid to differ per atom 

    - Increases time efficiency
    @Ali-Tehrani
    Ali-Tehrani committed Jun 24, 2023
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Commits on Sep 14, 2023

  1. Fix saving surface qtaim for python 3.8

    @Ali-Tehrani
    Ali-Tehrani committed Sep 14, 2023
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  2. Add option to include optional degree 

    - Can create any angular degree
    @Ali-Tehrani
    Ali-Tehrani committed Sep 14, 2023
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  3. Add annotating maximas in plotting 

    Easier to track atoms
    @Ali-Tehrani
    Ali-Tehrani committed Sep 14, 2023
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  4. Fix isosurface points problem

    @Ali-Tehrani
    Ali-Tehrani committed Sep 14, 2023
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Commits on Sep 25, 2023

  1. Add getting surfaces of atoms

    @Ali-Tehrani
    Ali-Tehrani committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. Add print statement and increase maxiter 

    For finding NNA
    Ali-Tehrani committed Sep 26, 2023
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  2. Add no refinement if not enough points on OAS

    Ali-Tehrani committed Sep 26, 2023
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  3. Decrease beta-sphere when NNA are found 

    - The NNA was incredibly close and so the beta-sphere must
have been decreased
    Ali-Tehrani committed Sep 26, 2023
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  4. Add option for having minimal radial point to API

    Ali-Tehrani committed Sep 26, 2023
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Commits on Sep 29, 2023

  1. Fix bug in getting IAS and surface points 

    - np.unique doesn't preserve order
    @Ali-Tehrani
    Ali-Tehrani committed Sep 29, 2023
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  2. Update parameter variables to make it more clear

    @Ali-Tehrani
    Ali-Tehrani committed Sep 29, 2023
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  3. Fix radial grids to use all maximas

    @Ali-Tehrani
    Ali-Tehrani committed Sep 29, 2023
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  4. Add second method of obtaining group of surfaces

    @Ali-Tehrani
    Ali-Tehrani committed Sep 29, 2023
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  5. Merge branch 'qtaim' of https://github.com/Ali-Tehrani/chemtools into… 

    … qtaim
    @Ali-Tehrani
    Ali-Tehrani committed Sep 29, 2023
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Commits on Oct 18, 2023

  1. Add surface partitioning to Hirshfeld

    @Ali-Tehrani
    Ali-Tehrani committed Oct 18, 2023
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Commits on Oct 23, 2023

  1. 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 committed Oct 23, 2023
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Commits on Nov 7, 2023

  1. Add negative indices check 

    - only for surface atoms, because it doesn't work with negative
  indices
    @Ali-Tehrani
    Ali-Tehrani committed Nov 7, 2023
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  2. Add list to numpy array

    Ali-Tehrani committed Nov 7, 2023
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Commits on Nov 22, 2023

  1. Add linalg error catching to crtical_pt finder

    @Ali-Tehrani
    Ali-Tehrani committed Nov 22, 2023
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Commits on Feb 20, 2024

  1. Change correct type for later numpy

    Ali-Tehrani committed Feb 20, 2024
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  2. Fix bug in final bad rays

    Ali-Tehrani committed Feb 20, 2024
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Commits on May 10, 2024

  1. Update to new grid api for angulargrid

    @Ali-Tehrani
    Ali-Tehrani committed May 10, 2024
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Commits on May 23, 2024

  1. Add to utils hirshfeld surface finder 

    - Need this for refinement within Surface class
    @Ali-Tehrani
    Ali-Tehrani committed May 23, 2024
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  2. Add refinement to hirshfeld type methods

    @Ali-Tehrani
    Ali-Tehrani committed May 23, 2024
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