Transformed cube (#15) #96
Commits on May 29, 2020
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Add coordinate promolecular transformation (theochem#15)
Added the transformation from real space to unit cube using the Promolecular density function of a single coordinate. Added the inverse transformation from unit-cube to real space using a root-solver of a single coordinate.
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Add promol cubic class and grid transform (theochem#15)
* Promolecular Cubic Grid Transformation is added. * Bracket initalization is added as private func. * Padding multiple arrays with zeros is added st have array size. * Full Grid transformation from unit-cube to real space.
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Add promolecular density evaluation (theochem#15)
Need this for integration
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Add integration method to promol transform (theochem#15)
Also added the promolecular trick.
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Commits on May 31, 2020
Commits on Jun 12, 2020
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Add jacobian and steepest ascent to promol transf
Follows changes were made - Added and Fixed docuentation. - Added jacobian of transformation - Added steepest-ascent - Added utility to transform individual points
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Commits on Jun 17, 2020
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Add promolecular density dataclass
Private data class that holds the coefficients, exponents, dimensions and compute its density.
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Remove helper function in inverse_coordinate
From code review, it was not necessary.
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Change stepsize to number of points for input
Providing number of points seems more natural than providing the stepsize for Promolecular Cubic, Uniform Grid Transformation.
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Add mask to small/nan values for integrate promol
Code review suggestion to use masked arrays for boundary points and small values of promolecular with a user-defined tolerance.
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Add dynamic bracketing method to root eqn
Suggested in code review, able to handle insufficient brackets.
Commits on Jun 20, 2020
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Add cubic grid support for protransform
Cubic grid is a tensor product of one-dimensional grids. Promolecular transform is modeled on a cubic grid.
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Change default [0, 1] to [-1, 1] for Promolecular
Since the bounds [-1, 1] is used in onedgrids.py, the default bounds is changed to be consistent.
Commits on Jun 21, 2020
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Add integration test for promolecular transform
Since cubic grids are not supported, I tested integration with GaussChebslev oned grid.
Commits on Jun 26, 2020
Commits on Jul 6, 2020
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Add hessian and interpolation to grid transform
Added - convert index to indices to grid transform - convert indices to index to grid transform - interpolation and its derivative - hessian
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Commits on Jul 7, 2020
Commits on Aug 5, 2020
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Update setup.py to use dataclass in 3.6
dataclass is included in python3.7. Acknowledgement to Derrick
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Add parameter to doc of interpolation
Also removed an if statement that wasnt really needed and to improve coverage
Commits on May 12, 2023
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Merge branch 'master' of https://github.com/Ali-Tehrani/grid into tra…
…nsformed_cube
Commits on May 15, 2023
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Group pytest parameterize test in protrans
- Makes it easier for viewing and generalizes some test to work over a wider range of points
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Generalize Promol For HyperRectangle class
- Makes it consistent for the cubic grid class
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Fix interpolate in cubic to not include boundary
Useful for promolecular transformation
Commits on May 16, 2023
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Add grid_pts option to interpolate
- Useful for promolecular transform where the grid to interpolate is different - Make inteprolate its own function due to problems with sub-classing in python
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Add cut-off for promolecular transform
- Needed to say a point is on the boundary
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Update interpolation in promolecular transform
- Matches the HyperRectangle class
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Add error raise if couldn't solve for inverse
- For promolecular transform
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Merge branch 'transformed_cube' of https://github.com/Ali-Tehrani/grid …
…into transformed_cube