Transformed cube (#15) #96

Ali-Tehrani · 2020-06-12T21:17:38Z

Promolecular Transformation of a Cubic grid class. This is regarding issue #15.

Functionality

Transform Cubic Grid in [0,1]^3 to R^3 using promolecular.
Transform individual points.
Integration (has weak tests).
Jacobian of Transformation.
Steepest-ascent of a function in Theta space.
Directional derivatives in Theta space (Not Tested).
Instead of [0,1]^3, change to [-1, 1]^3 and in docs (a35a07e).
Added dynamic bracketing (b8fc2b2).
Added Cubic Grid as Tensor Product of OneD grids (c104ac6).
Added tolerance and using masked arrays for integration (eb32897).
Hessian of transformation (9e73400)
Interpolation and Derivative Interpolation (8727c0a).
Python dataclass is not in py36 (187c00e).

TODO

Make/Reduce tests faster
Vectorize Logarithm Interpoaltion
Test for Directional Derivative.

May 16, 2023. All of the TODO except for the "Directional derivative tests" are now fixed/added.

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.

* 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.

Need this for integration

Also added the promolecular trick.

Follows changes were made - Added and Fixed docuentation. - Added jacobian of transformation - Added steepest-ascent - Added utility to transform individual points

codecov · 2020-06-12T21:19:40Z

Codecov Report

Attention: 14 lines in your changes are missing coverage. Please review.

Comparison is base (df822cf) 100.00% compared to head (187c00e) 99.12%.
Report is 268 commits behind head on master.

❗ Current head 187c00e differs from pull request most recent head 435577e. Consider uploading reports for the commit 435577e to get more accurate results

Files	Patch %	Lines
src/grid/protransform.py	95.30%	14 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##            master      #96      +/-   ##
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- Coverage   100.00%   99.12%   -0.88%     
===========================================
  Files           14       14              
  Lines         1385     1592     +207     
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+ Hits          1385     1578     +193     
- Misses           0       14      +14

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Private data class that holds the coefficients, exponents, dimensions and compute its density.

From code review, it was not necessary.

Providing number of points seems more natural than providing the stepsize for Promolecular Cubic, Uniform Grid Transformation.

Code review suggestion to use masked arrays for boundary points and small values of promolecular with a user-defined tolerance.

Suggested in code review, able to handle insufficient brackets.

Cubic grid is a tensor product of one-dimensional grids. Promolecular transform is modeled on a cubic grid.

Since the bounds [-1, 1] is used in onedgrids.py, the default bounds is changed to be consistent.

Since cubic grids are not supported, I tested integration with GaussChebslev oned grid.

Added - convert index to indices to grid transform - convert indices to index to grid transform - interpolation and its derivative - hessian

dataclass is included in python3.7. Acknowledgement to Derrick

Also removed an if statement that wasnt really needed and to improve coverage

FarnazH · 2021-08-31T01:37:54Z

@Ali-Tehrani does this need to be dusted off after the cubic grid is merged? If not, is it ready to be reviewed?

PaulWAyers · 2023-05-04T17:50:31Z

Integrate this with the cubic grid class.
Address Transformed Cubic Grid #15

…nsformed_cube

- Makes it easier for viewing and generalizes some test to work over a wider range of points

- Makes it consistent for the cubic grid class

Useful for promolecular transformation

- Useful for promolecular transform where the grid to interpolate is different - Make inteprolate its own function due to problems with sub-classing in python

- Needed to say a point is on the boundary

- Increases generality

- Matches the HyperRectangle class

- For promolecular transform

Ali-Tehrani · 2023-05-16T13:30:32Z

Added new changes:

It is a subclass of the base-class Hyper-Rectangle class in cubic
Interpolation in cubic.py only worked for a single point when use_log=True and derivatives are wanted. This is now fixed and the tests were updated.
Promolecular Transform Tests were updated, improved and randomized over a grid of points rather than a fixed set.
Interpolation with Promol Transform now works.
The requirement that promolecular transform requires boundary is removed and now works over any grid

…into transformed_cube

Ali-Tehrani added 10 commits May 29, 2020 09:16

Add coordinate promolecular transformation (theochem#15)

87626d2

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.

Add promol cubic class and grid transform (theochem#15)

fbe5355

* 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.

Add promolecular density evaluation (theochem#15)

8b1e12b

Need this for integration

Add integration method to promol transform (theochem#15)

815096e

Also added the promolecular trick.

Add docs to promolecular grid transform (theochem#15)

42efb07

Fix black complaints

aebc519

Fix integration method for promol transform (theochem#15)

8e37b8c

Add tests to promolecular grid transformation

775466f

Add jacobian and steepest ascent to promol transf

a79ee45

Follows changes were made - Added and Fixed docuentation. - Added jacobian of transformation - Added steepest-ascent - Added utility to transform individual points

Fix black issue

809f68c

Ali-Tehrani added 17 commits June 17, 2020 13:16

Add promolecular density dataclass

50f9a73

Private data class that holds the coefficients, exponents, dimensions and compute its density.

Add docs to _root_equation for promol transform

ad01358

Remove helper function in inverse_coordinate

11b603a

From code review, it was not necessary.

Change stepsize to number of points for input

239858b

Providing number of points seems more natural than providing the stepsize for Promolecular Cubic, Uniform Grid Transformation.

Add mask to small/nan values for integrate promol

eb32897

Code review suggestion to use masked arrays for boundary points and small values of promolecular with a user-defined tolerance.

Rename coords to indices

40a0487

Add dynamic bracketing method to root eqn

b8fc2b2

Suggested in code review, able to handle insufficient brackets.

Add cubic grid support for protransform

c104ac6

Cubic grid is a tensor product of one-dimensional grids. Promolecular transform is modeled on a cubic grid.

Change default [0, 1] to [-1, 1] for Promolecular

a35a07e

Since the bounds [-1, 1] is used in onedgrids.py, the default bounds is changed to be consistent.

Add integration test for promolecular transform

ab7cd82

Since cubic grids are not supported, I tested integration with GaussChebslev oned grid.

Add Hessian and tests promolecular

9e73400

Add hessian and interpolation to grid transform

8727c0a

Added - convert index to indices to grid transform - convert indices to index to grid transform - interpolation and its derivative - hessian

Add test for hessian and interpolation promol

f21aa78

Add documentation to Promolecular

a6f0a96

Update setup.py to use dataclass in 3.6

4d56f35

dataclass is included in python3.7. Acknowledgement to Derrick

Update integrand doc in promol

187c00e

Add parameter to doc of interpolation

7d420e4

Also removed an if statement that wasnt really needed and to improve coverage

FarnazH requested review from tczorro and FarnazH August 12, 2020 18:53

FarnazH requested a review from tovrstra August 12, 2020 18:53

Ali-Tehrani added 15 commits May 12, 2023 15:43

Merge branch 'master' of https://github.com/Ali-Tehrani/grid into tra…

1f4a0e7

…nsformed_cube

Rename interpolation

fd69714

Group pytest parameterize test in protrans

012f52b

- Makes it easier for viewing and generalizes some test to work over a wider range of points

Generalize Promol For HyperRectangle class

717649d

- Makes it consistent for the cubic grid class

Remove doc in protransform test

9fc1a13

Change np.nan to infinity

a5c9f8a

Fix interpolate in cubic to not include boundary

a6e60ba

Useful for promolecular transformation

Add grid_pts option to interpolate

53fa689

- Useful for promolecular transform where the grid to interpolate is different - Make inteprolate its own function due to problems with sub-classing in python

Fix interpolate in cubic with log is vectorized

fa43c9d

Add cut-off for promolecular transform

0d75416

- Needed to say a point is on the boundary

Add lower and upper bound to promolecular

3a48432

- Increases generality

Update interpolation in promolecular transform

d52ec8b

- Matches the HyperRectangle class

Add error raise if couldn't solve for inverse

adacc37

- For promolecular transform

Remove requirement for boundary in promoltransf

791fb4a

Update interpolation tests in promol transf

7cf98c5

Ali-Tehrani added 3 commits May 16, 2023 09:31

Merge branch 'master' into transformed_cube

a9f2a85

Remove TODO in promol transform

cc4625e

Merge branch 'transformed_cube' of https://github.com/Ali-Tehrani/grid …

435577e

…into transformed_cube

FarnazH added the enhancement New feature or request label Oct 26, 2023

FarnazH removed the request for review from tczorro November 17, 2023 15:34

FarnazH added the future feature New feature that is coming soon label Jan 3, 2024

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Transformed cube (#15) #96

Transformed cube (#15) #96

Ali-Tehrani commented Jun 12, 2020 •

edited

codecov bot commented Jun 12, 2020 •

edited

FarnazH commented Aug 31, 2021

PaulWAyers commented May 4, 2023 •

edited by FarnazH

Ali-Tehrani commented May 16, 2023

Transformed cube (#15) #96

Are you sure you want to change the base?

Transformed cube (#15) #96

Conversation

Ali-Tehrani commented Jun 12, 2020 • edited

Functionality

TODO

codecov bot commented Jun 12, 2020 • edited

Codecov Report

FarnazH commented Aug 31, 2021

PaulWAyers commented May 4, 2023 • edited by FarnazH

Ali-Tehrani commented May 16, 2023

Ali-Tehrani commented Jun 12, 2020 •

edited

codecov bot commented Jun 12, 2020 •

edited

PaulWAyers commented May 4, 2023 •

edited by FarnazH