Use pennylane numpy in molecular hamiltonian #2465

soranjh · 2022-04-20T15:32:01Z

Context:
This PR converts atomic coordinates to pennylane numpy arrays in molecular_hamiltonian function and returns real Hamiltonian coefficients.

Description of the Change:

Benefits:
Necessary to make some demos run:

Possible Drawbacks:

Related GitHub Issues:

github-actions · 2022-04-20T15:32:19Z

Hello. You may have forgotten to update the changelog!
Please edit doc/releases/changelog-dev.md with:

A one-to-two sentence description of the change. You may include a small working example for new features.
A link back to this PR.
Your name (or GitHub username) in the contributors section.

codecov · 2022-04-20T16:01:53Z

Codecov Report

❗ No coverage uploaded for pull request base (v0.23.0-rc0@089bb29). Click here to learn what that means.
The diff coverage is n/a.

@@              Coverage Diff               @@
##             v0.23.0-rc0    #2465   +/-   ##
==============================================
  Coverage               ?   99.47%           
==============================================
  Files                  ?      244           
  Lines                  ?    19452           
  Branches               ?        0           
==============================================
  Hits                   ?    19350           
  Misses                 ?      102           
  Partials               ?        0

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 089bb29...88d0304. Read the comment docs.

…o qchem_pl_numpy

antalszava

Looks good 🎉 Thank you.

pennylane/qchem/openfermion_obs.py

* Remove deprecated `get_unitary_matrix` (#2457) * Remove * Changelog * changelog: breaking change * Trigger CI Co-authored-by: Antal Szava <antalszava@gmail.com> * Rename `doc/releases/changelog-dev.md` → `doc/releases/changelog-0.23.0.md` (release candidate) (#2461) * changelog rename * update ref of the file * Fix the issue with JAX JIT for grad when `diff_method="adjoint"` and `mode="backward"` (#2460) * Fix the issue * Apply code review suggestions * Update changelog * Update jax.py * Trigger CI * Bugfix for Nesterov Momentum Optimier (#2466) * nesterov_fix * nesterov momentum bugfix * Update doc/releases/changelog-0.23.0.md * Update tests/optimize/test_optimize.py * Use pennylane numpy in molecular hamiltonian (#2465) * fix pl numpy and ham complex coeff * test * PR num * test tidy * correct method for returning real coeffs * linting Co-authored-by: Antal Szava <antalszava@gmail.com> * Remove `qml.finite_diff` (#2464) * remove finite-diff * remove unused import * Update doc/releases/changelog-0.23.0.md Co-authored-by: antalszava <antalszava@gmail.com> * remove hamiltonian diff test file Co-authored-by: antalszava <antalszava@gmail.com> * Update qchem documentation (#2454) * exclude files from pr * exclude more files Co-authored-by: Romain Moyard <rmoyard@gmail.com> Co-authored-by: Antal Szava <antalszava@gmail.com> Co-authored-by: Ali Asadi <ali@xanadu.ai> Co-authored-by: Christina Lee <christina@xanadu.ai> Co-authored-by: soranjh <40344468+soranjh@users.noreply.github.com> Co-authored-by: GitHub Actions Bot <> Co-authored-by: dime10 <dime10@users.noreply.github.com>

* Remove deprecated `get_unitary_matrix` (#2457) * Remove * Changelog * changelog: breaking change * Trigger CI Co-authored-by: Antal Szava <antalszava@gmail.com> * Rename `doc/releases/changelog-dev.md` → `doc/releases/changelog-0.23.0.md` (release candidate) (#2461) * changelog rename * update ref of the file * Fix the issue with JAX JIT for grad when `diff_method="adjoint"` and `mode="backward"` (#2460) * Fix the issue * Apply code review suggestions * Update changelog * Update jax.py * Trigger CI * Bugfix for Nesterov Momentum Optimier (#2466) * nesterov_fix * nesterov momentum bugfix * Update doc/releases/changelog-0.23.0.md * Update tests/optimize/test_optimize.py * Use pennylane numpy in molecular hamiltonian (#2465) * fix pl numpy and ham complex coeff * test * PR num * test tidy * correct method for returning real coeffs * linting Co-authored-by: Antal Szava <antalszava@gmail.com> * Remove `qml.finite_diff` (#2464) * remove finite-diff * remove unused import * Update doc/releases/changelog-0.23.0.md Co-authored-by: antalszava <antalszava@gmail.com> * remove hamiltonian diff test file Co-authored-by: antalszava <antalszava@gmail.com> * Update qchem documentation (#2454) * fix mera formatting issues (#2470) * Fix qcut doc render (#2471) * Update * Update * Trigger CI * fix has_matrix (#2476) * use qml.eigvals because MeasurementProcess.eigvals is being deprecated and raises a warning (#2477) * exclude files from pr * exclude more files Co-authored-by: Romain Moyard <rmoyard@gmail.com> Co-authored-by: Antal Szava <antalszava@gmail.com> Co-authored-by: Ali Asadi <ali@xanadu.ai> Co-authored-by: Christina Lee <christina@xanadu.ai> Co-authored-by: soranjh <40344468+soranjh@users.noreply.github.com> Co-authored-by: GitHub Actions Bot <> Co-authored-by: dime10 <dime10@users.noreply.github.com>

* Remove deprecated `get_unitary_matrix` (#2457) * Remove * Changelog * changelog: breaking change * Trigger CI Co-authored-by: Antal Szava <antalszava@gmail.com> * Rename `doc/releases/changelog-dev.md` → `doc/releases/changelog-0.23.0.md` (release candidate) (#2461) * changelog rename * update ref of the file * Fix the issue with JAX JIT for grad when `diff_method="adjoint"` and `mode="backward"` (#2460) * Fix the issue * Apply code review suggestions * Update changelog * Update jax.py * Trigger CI * Bugfix for Nesterov Momentum Optimier (#2466) * nesterov_fix * nesterov momentum bugfix * Update doc/releases/changelog-0.23.0.md * Update tests/optimize/test_optimize.py * Use pennylane numpy in molecular hamiltonian (#2465) * fix pl numpy and ham complex coeff * test * PR num * test tidy * correct method for returning real coeffs * linting Co-authored-by: Antal Szava <antalszava@gmail.com> * Remove `qml.finite_diff` (#2464) * remove finite-diff * remove unused import * Update doc/releases/changelog-0.23.0.md Co-authored-by: antalszava <antalszava@gmail.com> * remove hamiltonian diff test file Co-authored-by: antalszava <antalszava@gmail.com> * Update qchem documentation (#2454) * fix mera formatting issues (#2470) * Fix qcut doc render (#2471) * Update * Update * Trigger CI * fix has_matrix (#2476) * use qml.eigvals because MeasurementProcess.eigvals is being deprecated and raises a warning (#2477) * Warn upon import of an `ObservableReturnType` from operation instead of measurements (#2481) * warn upon import of observablereturntype from operation * black? * Update pennylane/__init__.py Co-authored-by: antalszava <antalszava@gmail.com> * Update tests/test_operation.py Co-authored-by: antalszava <antalszava@gmail.com> * update changelog * Update pennylane/operation.py Co-authored-by: antalszava <antalszava@gmail.com> * Update chemistry doc (#2482) * Automatic upload to pip when released (#2484) * upload * Return line * Jacobian Slice Bug StrawberryFields (#2485) * fixed jacobian slicing issue Update pennylane/interfaces/autograd.py Co-authored-by: antalszava <antalszava@gmail.com> * added testcase for custom device * Update doc/releases/changelog-0.23.0.md * retrigger checks Co-authored-by: antalszava <antalszava@gmail.com> * Documentation fixes for the v0.23.0 release (#2472) * Fix qml.ctrl docstring * Add notice about control values other than 0,1 * Fix bell example on measurements docs page * Update doc/introduction/measurements.rst Co-authored-by: Christina Lee <christina@xanadu.ai> * Update pennylane/transforms/control.py Co-authored-by: Christina Lee <christina@xanadu.ai> * Make the cut_circuit_mc docs example deterministic * Fix sphinx build Co-authored-by: Christina Lee <christina@xanadu.ai> Co-authored-by: antalszava <antalszava@gmail.com> * Issue a warning about repeated cached executions with shot noise (#2478) * Add warning about caching with finite shots * Fix import order * Add changelog * Use set_shots to determine shots for warning * format * disable pylint 'protected-access' * Fixes and cleanup to the inspection logic * format * add test for warning * Review: expand warning message * Review: add additional tests Co-authored-by: antalszava <antalszava@gmail.com> * exclude files from pr * Exclude more files Co-authored-by: Romain Moyard <rmoyard@gmail.com> Co-authored-by: Antal Szava <antalszava@gmail.com> Co-authored-by: Ali Asadi <ali@xanadu.ai> Co-authored-by: Christina Lee <christina@xanadu.ai> Co-authored-by: soranjh <40344468+soranjh@users.noreply.github.com> Co-authored-by: Sam Banning <samcbanning@gmail.com> Co-authored-by: David Ittah <dime10@users.noreply.github.com> Co-authored-by: GitHub Actions Bot <>

* Remove deprecated `get_unitary_matrix` (#2457) * Remove * Changelog * changelog: breaking change * Trigger CI Co-authored-by: Antal Szava <antalszava@gmail.com> * Rename `doc/releases/changelog-dev.md` → `doc/releases/changelog-0.23.0.md` (release candidate) (#2461) * changelog rename * update ref of the file * Fix the issue with JAX JIT for grad when `diff_method="adjoint"` and `mode="backward"` (#2460) * Fix the issue * Apply code review suggestions * Update changelog * Update jax.py * Trigger CI * Bugfix for Nesterov Momentum Optimier (#2466) * nesterov_fix * nesterov momentum bugfix * Update doc/releases/changelog-0.23.0.md * Update tests/optimize/test_optimize.py * Use pennylane numpy in molecular hamiltonian (#2465) * fix pl numpy and ham complex coeff * test * PR num * test tidy * correct method for returning real coeffs * linting Co-authored-by: Antal Szava <antalszava@gmail.com> * Remove `qml.finite_diff` (#2464) * remove finite-diff * remove unused import * Update doc/releases/changelog-0.23.0.md Co-authored-by: antalszava <antalszava@gmail.com> * remove hamiltonian diff test file Co-authored-by: antalszava <antalszava@gmail.com> * Update qchem documentation (#2454) * fix mera formatting issues (#2470) * Fix qcut doc render (#2471) * Update * Update * Trigger CI * fix has_matrix (#2476) * use qml.eigvals because MeasurementProcess.eigvals is being deprecated and raises a warning (#2477) * Warn upon import of an `ObservableReturnType` from operation instead of measurements (#2481) * warn upon import of observablereturntype from operation * black? * Update pennylane/__init__.py Co-authored-by: antalszava <antalszava@gmail.com> * Update tests/test_operation.py Co-authored-by: antalszava <antalszava@gmail.com> * update changelog * Update pennylane/operation.py Co-authored-by: antalszava <antalszava@gmail.com> * Update chemistry doc (#2482) * Automatic upload to pip when released (#2484) * upload * Return line * Jacobian Slice Bug StrawberryFields (#2485) * fixed jacobian slicing issue Update pennylane/interfaces/autograd.py Co-authored-by: antalszava <antalszava@gmail.com> * added testcase for custom device * Update doc/releases/changelog-0.23.0.md * retrigger checks Co-authored-by: antalszava <antalszava@gmail.com> * Documentation fixes for the v0.23.0 release (#2472) * Fix qml.ctrl docstring * Add notice about control values other than 0,1 * Fix bell example on measurements docs page * Update doc/introduction/measurements.rst Co-authored-by: Christina Lee <christina@xanadu.ai> * Update pennylane/transforms/control.py Co-authored-by: Christina Lee <christina@xanadu.ai> * Make the cut_circuit_mc docs example deterministic * Fix sphinx build Co-authored-by: Christina Lee <christina@xanadu.ai> Co-authored-by: antalszava <antalszava@gmail.com> * Issue a warning about repeated cached executions with shot noise (#2478) * Add warning about caching with finite shots * Fix import order * Add changelog * Use set_shots to determine shots for warning * format * disable pylint 'protected-access' * Fixes and cleanup to the inspection logic * format * add test for warning * Review: expand warning message * Review: add additional tests Co-authored-by: antalszava <antalszava@gmail.com> * Fix QChem documentation (#2487) * Fix finite-shots/caching warning appearing internally for gradients (#2491) * Fix warning appearing internally for gradients * pylint: fix protected attribute * Add test for checking no warning is raised * V0.23.0 notes (#2474) * notes + version * sections * update examples * remove empty sections * has_matrix bug fix * Adding more PRs to the changelog * PR, extend contributors * Extend list of contributors * Update the order of entries * Add auto cutting example; reorg QChem * remove curr release from 0.22.2 header * formatting * fix link * Update * Trigger CI * Change code blooc * Typo * Update pennylane/transforms/optimization/pattern_matching.py Co-authored-by: antalszava <antalszava@gmail.com> * Update pennylane/transforms/optimization/pattern_matching.py Co-authored-by: antalszava <antalszava@gmail.com> * Update pennylane/transforms/optimization/pattern_matching.py Co-authored-by: antalszava <antalszava@gmail.com> * Update pennylane/transforms/optimization/pattern_matching.py Co-authored-by: antalszava <antalszava@gmail.com> * Addd seealso * modify the qchem section * Update doc/releases/changelog-0.23.0.md Co-authored-by: Josh Izaac <josh146@gmail.com> * Update doc/releases/changelog-0.23.0.md Co-authored-by: Josh Izaac <josh146@gmail.com> * Update doc/releases/changelog-0.23.0.md Co-authored-by: Josh Izaac <josh146@gmail.com> * Update doc/releases/changelog-0.23.0.md Co-authored-by: Josh Izaac <josh146@gmail.com> * code review * code review * code review (remove empty lines & add pattern matching opt docstring link) * Update doc/releases/changelog-0.23.0.md Co-authored-by: Josh Izaac <josh146@gmail.com> * Update doc/releases/changelog-0.23.0.md Co-authored-by: Josh Izaac <josh146@gmail.com> * shape and numeric type example * MP description update * rephrase expand_strategy for qml.specs improvement * update * caching phrasing * removed * phrasing * updates * bug phrasing, reorder * update link placement and use pycon * include swap test output in example * More info on HS template * rephrase QCut * move example to UsageDetails * auto QCut rephrase * More powerful circuit cutting * Trigger CI * Upddate * add qchem code example * correct typo in qchem text * no backticks * fix the case when obs=None for a MeasurementProcess for interface selection * update * changelog * docstring * Update doc/releases/changelog-0.23.0.md Co-authored-by: Josh Izaac <josh146@gmail.com> * update links as per code review * typo * pycon syntax * double backticks * no dev in release header * Lightning v0.23.0 required in setup.py Co-authored-by: Romain Moyard <rmoyard@gmail.com> Co-authored-by: soranjh <soranjh@yahoo.com> Co-authored-by: Josh Izaac <josh146@gmail.com> * Remove typo * Update pennylane/interfaces/jax.py Co-authored-by: Romain Moyard <rmoyard@gmail.com> Co-authored-by: Ali Asadi <ali@xanadu.ai> Co-authored-by: Christina Lee <christina@xanadu.ai> Co-authored-by: soranjh <40344468+soranjh@users.noreply.github.com> Co-authored-by: Sam Banning <samcbanning@gmail.com> Co-authored-by: David Ittah <dime10@users.noreply.github.com> Co-authored-by: Josh Izaac <josh146@gmail.com> Co-authored-by: soranjh <soranjh@yahoo.com>

fix pl numpy and ham complex coeff

0fee365

antalszava mentioned this pull request Apr 20, 2022

Update spsa PennyLaneAI/qml#464

Merged

soranjh and others added 5 commits April 20, 2022 14:06

Merge branch 'v0.23.0-rc0' into qchem_pl_numpy

8b30f77

test

01adb92

Merge branch 'qchem_pl_numpy' of github.com:PennyLaneAI/pennylane int…

807edfa

…o qchem_pl_numpy

PR num

94ca395

test tidy

ce1c6f9

antalszava approved these changes Apr 20, 2022

View reviewed changes

correct method for returning real coeffs

f12b50d

antalszava mentioned this pull request Apr 20, 2022

Fix QChem related demo errors, get latest Lightning & pin Cirq PennyLaneAI/qml#467

Merged

linting

88d0304

antalszava reviewed Apr 20, 2022

View reviewed changes

pennylane/qchem/openfermion_obs.py Show resolved Hide resolved

antalszava reviewed Apr 20, 2022

View reviewed changes

pennylane/qchem/openfermion_obs.py Show resolved Hide resolved

antalszava merged commit 8558ce9 into v0.23.0-rc0 Apr 20, 2022

antalszava deleted the qchem_pl_numpy branch April 20, 2022 21:54

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Use pennylane numpy in molecular hamiltonian #2465

Use pennylane numpy in molecular hamiltonian #2465

soranjh commented Apr 20, 2022 •

edited by antalszava

Loading

github-actions bot commented Apr 20, 2022

codecov bot commented Apr 20, 2022 •

edited

Loading

antalszava left a comment

Use pennylane numpy in molecular hamiltonian #2465

Use pennylane numpy in molecular hamiltonian #2465

Conversation

soranjh commented Apr 20, 2022 • edited by antalszava Loading

github-actions bot commented Apr 20, 2022

codecov bot commented Apr 20, 2022 • edited Loading

Codecov Report

antalszava left a comment

Choose a reason for hiding this comment

soranjh commented Apr 20, 2022 •

edited by antalszava

Loading

codecov bot commented Apr 20, 2022 •

edited

Loading