Ground state solver (upper-bound problem formulation) #343

qchempku2017 · 2023-03-09T01:24:44Z

Summary

Enables formulating a ground state upper-bound problem from Ensemble.
Enables setting composition constraints in CompositionSpace from a string of equations, which should be more convenient.

Additional dependencies introduced (if any)

SCIP, pysciopt (For solving non-linear MIP problems).

Checklist

Code is in the standard Python style.
Run pycodestyle and flake8
on your local machine.
Docstrings have been added in the Google docstring format.
Run pydocstyle on your code.
Tests have been added for any new functionality or bug fixes.
All existing tests pass.

…nd problem generator.

…arent class.

… representations as well. Ongoing.

… Updated settings and docs in composition.py accordingly.

…ndling splitted sub-lattices and manually restricted sites. Ready to make tests.

…per_bound tests.

…r constraints and objectives.

… generation from using table to using orbits and decomposition objects. Need to add linearization for cvxpy to work.

…ts afterwards.

… objectives.

for more information, see https://pre-commit.ci

lbluque

Thanks so much for the hard work on this! It is starting to look pretty good. Apart from the inline comments, I have some overall comments:

I think you should use a simpler composition space in the jupyter notebook example. Since it is just a complex disordered structure you are only solving for a supercell of two unit cells. I think for the example it's better to have a simpler space and do a larger supercell.

I think we should mention in both the example and in the documentation (docstrings of Solver), that scaling is very poor because variables and constraints grow very rapidly.

smol/capp/generate/groundstate/upper_bound/constraints.py

smol/moca/composition/constraints.py

smol/capp/generate/groundstate/solver.py

qchempku2017 · 2023-07-21T19:23:39Z

Thanks so much for the hard work on this! It is starting to look pretty good. Apart from the inline comments, I have some overall comments:

I think you should use a simpler composition space in the jupyter notebook example. Since it is just a complex disordered structure you are only solving for a supercell of two unit cells. I think for the example it's better to have a simpler space and do a larger supercell.

I think we should mention in both the example and in the documentation (docstrings of Solver), that scaling is very poor because variables and constraints grow very rapidly.

The composition space example will be changed accordingly.

# Conflicts: # docs/src/notebooks/finding-groundstates.ipynb

smol/capp/generate/groundstate/upper_bound/constraints.py

smol/moca/composition/constraints.py

smol/capp/generate/__init__.py

smol/capp/generate/groundstate/__init__.py

…ition-constraints.ipynb, modify finding-groundstates.ipynb.

for more information, see https://pre-commit.ci

docs/src/notebooks/setting-composition-constraints.ipynb

smol/capp/generate/groundstate/__init__.py

smol/capp/generate/groundstate/upper_bound/solver.py

for more information, see https://pre-commit.ci

…lity. Changed notebooks accordingly.

lbluque

Thanks so much @qchempku2017, this looks great!

I have a few suggestions for edits on the CompositionSpace class and example, but since it is not the bulk of this PR, I will address it in a separate issue.

qchempku2017 added 2 commits March 7, 2023 17:38

Start writing ground state solver utilities.

3cc9869

Finished writing upper-bound utilities. Prepare to write canonicals a…

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…nd problem generator.

qchempku2017 added the enhancement New feature or request label Mar 9, 2023

qchempku2017 requested a review from lbluque March 9, 2023 01:24

qchempku2017 assigned lbluque and qchempku2017 Mar 9, 2023

lbluque changed the title ~~Ground state solver (upper-bound problem formulation)~~ [WIP] Ground state solver (upper-bound problem formulation) Mar 9, 2023

lbluque marked this pull request as draft March 9, 2023 16:37

qchempku2017 and others added 18 commits March 13, 2023 17:04

Start writing ground state solver class for smol. Using Ensemble as p…

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…arent class.

Merge remote-tracking branch 'upstream/main' into gs_solver

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Merge branch 'main' into gs_solver

c4edd48

Move composition constraint manager to moca.utils. Will handle string…

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… representations as well. Ongoing.

Finished implementing CompositionConstraintManager in constraints.py.…

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… Updated settings and docs in composition.py accordingly.

Finish todos in constraints.py.

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Finished implementing ground state upper-bound solver. Now enables ha…

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…ndling splitted sub-lattices and manually restricted sites. Ready to make tests.

Merge branch 'main' into gs_solver

ec81b18

Correction to ewald term and chemical work coefficients.

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Written tests for composition constraints.

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Passed new tests for composition constraints.

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Moved most solver utilities to upper_bound main folder; Configured up…

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…per_bound tests.

Finished tests for variables and utilities in upper_bound. Writing fo…

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…r constraints and objectives.

Merge remote-tracking branch 'upstream/main' into gs_solver

bfa5ca5

Finished writing tests to solvers. Need to change objective functions…

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… generation from using table to using orbits and decomposition objects. Need to add linearization for cvxpy to work.

Linearization and orbit refactoring code finished. Need to change tes…

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…ts afterwards.

Updated tests to objectives and solver. Trying to pass tests.

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Merge remote-tracking branch 'upstream/main' into gs_solver

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qchempku2017 mentioned this pull request Apr 4, 2023

ensemble.restricted_sites #353

Closed

qchempku2017 added 3 commits April 4, 2023 18:31

Passed solver utilities tests. Ready for the rest.

b9c7108

Merge branch 'main' into gs_solver

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Passed variables and constraints. Need to correct species encoding in…

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… objectives.

qchempku2017 and others added 4 commits July 14, 2023 18:00

TST: add pickling test to GroundStateSolver.

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DOC: rename groundstate example notebook

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DOC: rename small edits to example

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lbluque requested changes Jul 20, 2023

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qchempku2017 added 2 commits July 21, 2023 15:36

DEV: Fixes issues in discussion.

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Merge remote-tracking branch 'origin/gs_solver' into gs_solver

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# Conflicts: # docs/src/notebooks/finding-groundstates.ipynb

qchempku2017 requested a review from lbluque July 21, 2023 22:39

FIX: Lint fix.

679743b

lbluque reviewed Jul 22, 2023

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qchempku2017 added 2 commits July 22, 2023 16:47

Merge remote-tracking branch 'upstream/main' into gs_solver

00b4812

DEV: change import order of UpperBoundSolver. DOC: add setting-compos…

bd2d853

…ition-constraints.ipynb, modify finding-groundstates.ipynb.

qchempku2017 requested a review from lbluque July 23, 2023 00:40

[pre-commit.ci] auto fixes from pre-commit.com hooks

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lbluque requested changes Jul 24, 2023

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docs/src/notebooks/setting-composition-constraints.ipynb Outdated Show resolved Hide resolved

smol/capp/generate/groundstate/__init__.py Outdated Show resolved Hide resolved

smol/capp/generate/groundstate/upper_bound/solver.py Outdated Show resolved Hide resolved

lbluque and others added 3 commits July 24, 2023 16:26

MAINT: minor change to import cvxpy

307c4c0

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DEV: Rename UpperBoundSolver to PeriodicGroundStateSolver for readabi…

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…lity. Changed notebooks accordingly.

qchempku2017 requested a review from lbluque July 25, 2023 03:08

lbluque added 5 commits July 25, 2023 15:31

DOC: edit example notebooks

a556d34

DOC: add ground-state API docs and edit capp entry

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DOC: add ground-state example notebook to docs

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DOC: use note and warning blocks in docstrings

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DEV: add sphinx autodoc type hints

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lbluque approved these changes Jul 25, 2023

View reviewed changes

fix missing comma

99ae137

lbluque changed the title ~~[WIP] Ground state solver (upper-bound problem formulation)~~ Ground state solver (upper-bound problem formulation) Jul 26, 2023

lbluque merged commit 3f1f8e4 into CederGroupHub:main Jul 26, 2023

qchempku2017 deleted the gs_solver branch September 13, 2023 19:42

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Ground state solver (upper-bound problem formulation) #343

Ground state solver (upper-bound problem formulation) #343

qchempku2017 commented Mar 9, 2023 •

edited by lbluque

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qchempku2017 commented Jul 21, 2023

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Ground state solver (upper-bound problem formulation) #343

Ground state solver (upper-bound problem formulation) #343

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qchempku2017 commented Mar 9, 2023 • edited by lbluque Loading

Summary

Additional dependencies introduced (if any)

Checklist

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qchempku2017 commented Jul 21, 2023

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qchempku2017 commented Mar 9, 2023 •

edited by lbluque

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