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Optimize2 #358

Merged
merged 110 commits into from
Apr 28, 2023
Merged

Optimize2 #358

merged 110 commits into from
Apr 28, 2023

Commits on Mar 16, 2023

  1. refactor utils into module

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    lbluque committed Mar 16, 2023
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  2. cython structs for array data and containers to hold a list of arrays

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    lbluque committed Mar 16, 2023
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  3. linting

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    lbluque committed Mar 16, 2023
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  4. refactor test_utils as a directory

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    lbluque committed Mar 16, 2023
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  5. add test for Containers

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    lbluque committed Mar 16, 2023
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  6. add test for orbitcontainer

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    lbluque committed Mar 16, 2023
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  7. int array containers

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Commits on Mar 17, 2023

  1. [wip] implementation of clusterspace evaluator (is segfaulting)

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    lbluque committed Mar 17, 2023
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  2. fixed evaluator

    @lbluque
    lbluque committed Mar 17, 2023
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  3. prange nogil in corr_from_occu

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    lbluque committed Mar 17, 2023
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Commits on Mar 20, 2023

  1. change array lists to tuples of arrays

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  2. interactions from occupancy in evaluator (2x faster)

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    lbluque committed Mar 20, 2023
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  3. move evaluator to cluster_utils

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    lbluque committed Mar 20, 2023
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Commits on Mar 21, 2023

  1. re-arrange loop variables

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    lbluque committed Mar 21, 2023
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  2. delta single flip functions in evaluator

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    lbluque committed Mar 21, 2023
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  3. fix remaining issues in localevaluator methods

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    lbluque committed Mar 21, 2023
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Commits on Mar 22, 2023

  1. keep number of correlations as OrbitContainer attribute

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    lbluque committed Mar 22, 2023
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  2. mark evaluator as final

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    lbluque committed Mar 22, 2023
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  3. only a single evaluator for local and global calcs

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    lbluque committed Mar 22, 2023
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  4. remove const in struct creation

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    lbluque committed Mar 22, 2023
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  5. save total number of corr and orbits in evaluator

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    lbluque committed Mar 22, 2023
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  6. save total number of corr and orbits in evaluator

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    lbluque committed Mar 22, 2023
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Commits on Mar 23, 2023

  1. keep python reference in containers

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    lbluque committed Mar 23, 2023
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  2. cluster_interactions as attribute in evaluator

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    lbluque committed Mar 23, 2023
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  3. use interaction_tensor attribute in calcs

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    lbluque committed Mar 23, 2023
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  4. rename delta_corr and delta_interactions

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  5. use named tuple to hold arrays and cython container of orbit indices

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    lbluque committed Mar 23, 2023
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  6. add clusterspacevaluator as private attribute in clustersubspace

    @lbluque
    lbluque committed Mar 23, 2023
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  7. add reset method to Evaluator and fix tests

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    lbluque committed Mar 23, 2023
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Commits on Mar 24, 2023

  1. use evaluator in clusterspace

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    lbluque committed Mar 24, 2023
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  2. move delta_ewald to cluster_utils

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    lbluque committed Mar 24, 2023
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  3. rename cluster_utils -> cluster

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    lbluque committed Mar 24, 2023
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  4. mark gen_orbit_list deprecated

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    lbluque committed Mar 24, 2023
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  5. use evaluator in CE processor

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    lbluque committed Mar 24, 2023
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  6. use evaluator in CD processor

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    lbluque committed Mar 24, 2023
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  7. fix CD processor as_dict

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    lbluque committed Mar 24, 2023
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  8. add cythonized C files

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    lbluque committed Mar 24, 2023
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Commits on Mar 27, 2023

  1. fix array container exceptions and tests

    @lbluque
    lbluque committed Mar 27, 2023
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  2. test orbitcontainer exceptions

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    lbluque committed Mar 27, 2023
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  3. use evaluator in subspace tests

    @lbluque
    lbluque committed Mar 27, 2023
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  4. test evaluator vs legacy

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    lbluque committed Mar 27, 2023
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  5. test interactions in evaluator vs legacy

    @lbluque
    lbluque committed Mar 27, 2023
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  6. fixes + TODO

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    lbluque committed Mar 27, 2023
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Commits on Mar 28, 2023

  1. use guided schedule for corr and interactions

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    lbluque committed Mar 28, 2023
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Commits on Mar 29, 2023

  1. use evaluator to compute interactions in CE

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  2. fix evaluator tests

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    lbluque committed Mar 29, 2023
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  3. create copy of subspace in expansion

    @lbluque
    lbluque committed Mar 29, 2023
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  4. fix comments in container

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    lbluque committed Mar 29, 2023
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  5. improvements to test_prune

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    lbluque committed Mar 29, 2023
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  6. allow passing site_mappings in predict

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  7. rename compute_cluster_interactions to cluster_interactions_from_stru… 

    …cture to match subspace style
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  8. instantiate new evaluators in processors

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  9. concatenate features in composite processor

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    lbluque committed Mar 29, 2023
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  10. add correlations.c file

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    lbluque committed Mar 29, 2023
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  11. delta_ewald as nogil

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    lbluque committed Mar 29, 2023
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  12. remove fopenmp flag from ewald

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Commits on Mar 30, 2023

  1. allow to set num_threads in clusterspace and processors

    @lbluque
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  2. rename SetThreads -> SetNumThreads

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    lbluque committed Mar 30, 2023
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  3. interface to set threads in processors

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    lbluque committed Mar 30, 2023
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Commits on Apr 11, 2023

  1. BLD: openmp check in build [wip]

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  2. BLD: check and get appropriate omp flags

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    lbluque committed Apr 11, 2023
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Commits on Apr 12, 2023

  1. MNT: reset evaluator when removing corrs

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  2. API: remove _get_orbit_data staticmethod and move to utils.cluster

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  3. BLD: cleanup and always cythonize setup.py

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    lbluque committed Apr 12, 2023
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  4. BLD: update dependency versions + add cython

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Commits on Apr 17, 2023

  1. TST: add test for setting num_threads in processors

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Commits on Apr 18, 2023

  1. ENH: _openmp_helpers to obtain valid number of threads

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  2. ENH: add _openmp_helpers.pyx

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  3. ENH: respect OMP_NUM_THREADS if set

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  4. Merge branch 'main' of https://github.com/CederGroupHub/smol into opt… 

    …imize2

� Conflicts:
�	smol/cofe/space/clusterspace.py
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  5. DEV: build.yml with macOS openmp support

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  6. DEV: fix build.yml

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    lbluque committed Apr 18, 2023
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  7. BLD: include cython and numpy in setup_requires

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  8. BLD: fix wheel building issues

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    lbluque committed Apr 18, 2023
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  9. BLD: fix build.yml

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    lbluque committed Apr 18, 2023
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  10. BLD: fix build.yml

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    lbluque committed Apr 18, 2023
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  11. BLD: remove parallelization in cythonize

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Commits on Apr 19, 2023

  1. DEV: add platform/arch in matrix build.yml

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  2. DEV: fix build.yml

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    lbluque committed Apr 19, 2023
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  3. STY: fix precommit

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    lbluque committed Apr 19, 2023
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  4. BLD: use pyproject.toml

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  5. DEV: move config to pyproject.toml

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  6. DEV: remove flake8 from lint.yml

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  7. TST: use Types for 3.8 compat

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  8. BUG: revert to appending in processor results

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  9. MAINT: set default threads to 2

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Commits on Apr 20, 2023

  1. DOC: example notebook for setting openmp threads

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Commits on Apr 21, 2023

  1. DEV: build macos wheels separately

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  2. DEV: fix build.yml

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  3. DEV: fix build.yml

    @lbluque
    lbluque committed Apr 21, 2023
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  4. DEV: fix build.yml

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  5. print os.environ to check build issue

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  6. print os.environ to check build issue

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  7. DEV: fix build.yml

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  8. DEV: set env variables in build.yml

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  9. debugging build.yml

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Commits on Apr 22, 2023

  1. debugging build.yml

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  2. BLD: set mcpu to apple-m1 if crosscompiling

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  3. DEV: adapt release.yml to build macos wheels with openmp

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  4. DOC: omp parallelism notebook

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Commits on Apr 26, 2023

  1. DOC: add installing from source in developer_guide

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  2. DOC: add openmp-parallelism.ipynb notebook to docs

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  3. DOC: add openmp-parallelism.ipynb to index.ipynb

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  4. Merge branch 'main' into optimize2

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  5. TST: fix test_flush_to_hdf5

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  6. STY: minor codacy fixes

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  7. TST: fix clustersubspace tests

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Commits on Apr 27, 2023

  1. API: rename descriptor.py -> setmany.py

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  2. MAINT: rename SMOL_OPENMP_ENABLED OPENMP_ENABLED

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Commits on Apr 28, 2023

  1. DEV: use flake8 with config directly in lint.yml

    @lbluque
    lbluque committed Apr 28, 2023
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