Code

Merge refactoring branch#2

Code

Merged

xiaochendu merged 161 commits intomasterlearningmatter-mit/surface-sampling:masterfrom refactoringlearningmatter-mit/surface-sampling:refactoringCopy head branch name to clipboardJul 18, 2024

+23,031-8,485

Commits

Commits on Feb 6, 2024

• new SurfaceSystem class

  xiaochendu

  committed
  586b0cf

Commits on Feb 9, 2024

• add custom surface energy calculators and refactor energy calculation

  xiaochendu

  committed
  8ddf04e

Commits on Feb 11, 2024

• implement LAMMMPSCalc and partial integration into energy.py

  xiaochendu

  committed
  bcdf043

• add TrajectoryObserver (not fully integrated yet)

  xiaochendu

  committed
  a5774ce

Commits on Feb 13, 2024

• comment out redundant code and bug fixes

  xiaochendu

  committed
  7b6a83a

Commits on Feb 14, 2024

• tidy up code and settings dicts

  xiaochendu

  committed
  3443db9

Commits on Mar 8, 2024

• algorithm sketches for acceptance criterion and event

  xiaochendu

  committed
  8afda37

Commits on Mar 12, 2024

• docstrings and offset units for Calculators

  xiaochendu

  committed
  7ce7c39

• save relaxation trajectories

  xiaochendu

  committed
  b3eb386

• fix initialize with occupation/states

  xiaochendu

  committed
  20b310e

• fix tutorials sampling with LAMMPS template and tests

  xiaochendu

  committed
  4a9c055

Commits on Mar 17, 2024

• active learning scripts in testing

  xiaochendu

  committed
  0ead273

Commits on Mar 20, 2024

• BLD: add clustering and related utils, move to new utils folder

  xiaochendu

  committed
  5643dfb

Commits on Mar 29, 2024

• BLD: add LAMMPSRunSurfCalc for lammpsrun way of calling LAMMPS

  xiaochendu

  committed
  2f7268b

• MAINT: standardize tutorial formats and test

  xiaochendu

  committed
  c83c399

• BLD: change get_atoms_batch helper function

  xiaochendu

  committed
  f36c52c

• MAINT: fix imports

  xiaochendu

  committed
  d9fbb97

• STY: remove commented out lines

  xiaochendu

  committed
  882f77c

• ENH & MAINT: refactor out some utility functions, standardize save_folder

  xiaochendu

  committed
  67782d7

• BLD: add sampling script example

  xiaochendu

  committed
  c480e23

• MAINT: change tests resources folder to data

  xiaochendu

  committed
  654edb2

• BUG: fix removed import (my bad)

  xiaochendu

  committed
  0e11f0c

Commits on Apr 9, 2024

• MAINT: standardize arguments and fix save path typo

  xiaochendu

  committed
  c3d3af2

Commits on Apr 19, 2024

• DOC: write docstrings for SurfaceSystem

  xiaochendu

  committed
  1bc125f

• MAINT: remove require_large_offsets

  xiaochendu

  committed
  c6946fe

• MAINT: move htvs perturbation method to project

  xiaochendu

  committed
  8582aca

• ENH: print full path of saved pkl

  xiaochendu

  committed
  ed83df4

• BLD: add general surface sampling script with PaiNN NFF

  xiaochendu

  committed
  6746519

Commits on Apr 26, 2024

• BUG: Fixed save path for mcmc calculations

  

  Eda Lozada

  committed
  d5cc884

Commits on Apr 30, 2024

• ENH: improve clustering speed by not using dense_nbrs

  xiaochendu

  committed
  acd9ad6

• MAINT: add final energy as output after ase relaxations

  xiaochendu

  committed
  fe7b57e

Commits on May 20, 2024

• ENH: moving energy calculation out of slab_energy

  xiaochendu

  committed
  ea8cd18

Commits on May 21, 2024

• REV: remove forces placeholder

  xiaochendu

  committed
  5470512

• ENH: remove slab_energy

  Show description for 117dcf9
  xiaochendu

  committed
  117dcf9

• BUG: fix SurfaceSystem.get_surface_energy

  Show description for 668e8b2
  xiaochendu

  committed
  668e8b2

Commits on May 22, 2024

• TST: update tests

  Show description for 3ddf996
  xiaochendu

  committed
  3ddf996

• DOC: update tutorials

  Show description for 04db037
  xiaochendu

  committed
  04db037

• TST: remove reference to personal directories

  xiaochendu

  committed
  d24165f

Commits on May 23, 2024

• MAINT & DOC: refactor change_site

  Show description for da046c3
  xiaochendu

  committed
  da046c3

• TST & DOC: update tests and tutorials

  xiaochendu

  committed
  85fd623

Commits on May 24, 2024

• ENH: change method of getting surface potential energies

  xiaochendu

  committed
  c32e8e8

• ENH: add staticmethod to save calculator results on call

  xiaochendu

  committed
  3669bd9

• MAINT & ENH: move semigrand sampling to separate Event, Proposal, and AcceptanceCriterion

  xiaochendu

  committed
  ffc4a28

Commits on May 26, 2024

• TST: wrote a lot more tests for various critical parts of the code

  Show description for 36413fe
  xiaochendu

  committed
  36413fe

• DOC & MAINT: improve docstrings and format, adding some checks

  xiaochendu

  committed
  f9232a1

• BUG: SurfaceSystem surface energy check and really allow no calc to be specified

  xiaochendu

  committed
  5a035c2

• BLD: initial Pourbaix sampling commit

  Show description for 27e0b1a
  xiaochendu

  committed
  27e0b1a

Commits on Jun 5, 2024

• BUG: use pymatgen data for consistency and change species concentrations

  xiaochendu

  committed
  45afc88

• DOC & BUG: update description to be more precise

  Show description for 1e72201
  xiaochendu

  committed
  1e72201

Commits on Jun 6, 2024

• MAINT: minor changes in kwargs for calc_settings

  xiaochendu

  committed
  8f81acb

Commits on Jun 7, 2024

• FEAT: Added Surface Depth to SurfaceSystem, merged with master

  

  Eda Lozada

  committed
  b2fb97b

Commits on Jun 14, 2024

• TEST: added tests for SurfaceSystem's surface_depth argument

  

  Eda Lozada

  committed
  bc0a9f1

Commits on Jun 15, 2024

• ENH & DOC: add SwitchProposal and update docstrings

  xiaochendu

  committed
  f56c492

• ENH & MAINT: add Exchange Event and move acceptance method to base class

  xiaochendu

  committed
  80f24ad

• ENH & MAINT: add backward method and minor docstring reformatting

  xiaochendu

  committed
  1fe9f91

• DOC & MAINT: add docstring to SwitchProposal, minor debugging and variable changes

  xiaochendu

  committed
  6af7d12

• BUG & MAINT: fix missing imports and minor variable changes

  xiaochendu

  committed
  692efef

• DEP: deprecate rmsd_criterion

  xiaochendu

  committed
  2ed9e4e

• ENH: refactor change_site_canonical to new SwitchProposal, Exchange Event, and AcceptanceCriterion's

  xiaochendu

  committed
  7bb3a29

Commits on Jun 17, 2024

• BUG: fix backward in Event

  xiaochendu

  committed
  ccf7a9c

• TST: add test_change_backward to test_event

  xiaochendu

  committed
  587b583

• DOC & MAINT: added docstring and type hints for slab.py and minor refacotring for slab.py and mcmc.py

  xiaochendu

  committed
  52ca925

Commits on Jun 19, 2024

• ENH & MAINT: Generalize Pourbaix sampling to different domains

  Show description for fd24079
  xiaochendu

  committed
  fd24079

• TST: added tests for PourbaixAtom generation

  xiaochendu

  committed
  c3222ce

• TST: add tests for Exchange Event and SwitchProposal

  xiaochendu

  committed
  e057719

Commits on Jun 20, 2024

• MAINT: improve save folder naming and run arguments

  Show description for 676ea47
  xiaochendu

  committed
  676ea47

• MAINT: improvements to constraints and specifying/generating adsorption sites

  Show description for 72168ec
  xiaochendu

  committed
  72168ec

• MAINT: surface layer adsorbates are included in adsorption sites with correct initial occ

  xiaochendu

  committed
  83c3c44

• STY: minor style changes

  xiaochendu

  committed
  69aff29

• MAINT: update SurfaceSystem intialization arguments

  xiaochendu

  committed
  445d9af

• BUG: fix self.num_pristine_atoms initialization in SurfaceSystem

  Show description for c4dbf20
  xiaochendu

  committed
  c4dbf20

• MAINT: refactor get_complementary_idx in slab.py

  xiaochendu

  committed
  930af4c

• MAINT: distance_weight_matrix moved into SurfaceSystem

  xiaochendu

  committed
  eb3fbd1

• TST: add tests for test_get_complementary_idx and helper function for distance-based and energy-based weights

  xiaochendu

  committed
  702f47c

Commits on Jun 21, 2024

• PERF: Changed calculator behavior for SurfaceSystem test cases

  

  Eda Lozada

  committed
  65243a0

Commits on Jun 22, 2024

• Merge branch 'master' into edaloz_surfsamp

  

  xiaochendu

  authored and

  GitHub Enterprise

  committed
  4e4a2bb

• Merge pull request #2 from MLMat/edaloz_surfsamp

  Show description for 0968cd6
  

  xiaochendu

  authored and

  GitHub Enterprise

  committed
  0968cd6

• DOC: add/correct docstrings for event.py and misc.py

  xiaochendu

  committed
  da6f3b1

• MAINT: per-atom energies are directly taken from calculator inside compute_boltzmann_weights

  xiaochendu

  committed
  a44fb9b

• MAINT: update Si 111 tutorial with distance decay and per atom energies

  xiaochendu

  committed
  8f73cda

• Merge remote-tracking branch 'origin/master' into refactoring

  xiaochendu

  committed
  d8c28f0

• TST: update tests and tutorials with new SurfaceSystem constraints

  xiaochendu

  committed
  d01bd47

• MAINT: remove large swaths of commented out sections in mcmc.py

  xiaochendu

  committed
  1fed72a

Commits on Jun 23, 2024

• MAINT: move save structure function after each MC sweep and after energy out of bounds to SurfaceSystem

  xiaochendu

  committed
  dddd7cd

• STY: ruff format test_system

  xiaochendu

  committed
  95885d1

• TST: update SurfaceSystem save and restore with atomic positions

  xiaochendu

  committed
  fc578c6

Commits on Jun 24, 2024

• ENH: add ads_pos_type as a system_settings parameter

  xiaochendu

  committed
  74aa62c

• DOC: reformatted system docstring from numpy to google style

  xiaochendu

  committed
  cd73143

• MAINT: added refactoring TODOs

  xiaochendu

  committed
  38959c3

Commits on Jun 25, 2024

• MAINT: create setup.py

  Show description for db4a6e3
  xiaochendu

  committed
  db4a6e3

Commits on Jun 26, 2024

• Merge branch 'refactoring' into pourbaix

  xiaochendu

  committed
  3ea6ef3

Commits on Jun 27, 2024

• MAINT: temporarily put back self.trajectories in MCMC object

  xiaochendu

  committed
  40cad7a

• BUG: fix test_system.py surface_system fixture after merging with refactoring branch

  xiaochendu

  committed
  9b19369

• MAINT: update sample_pourbaix_surface.py

  Show description for 47f7828
  xiaochendu

  committed
  47f7828

• DEP: deprecate get_adsorption_coords and remove it

  Show description for 580b5fa
  xiaochendu

  committed
  580b5fa

Commits on Jun 28, 2024

• MAINT & DOC: move create_anneal_schedule to utils/sampling.py

  Show description for 9f290c3
  xiaochendu

  committed
  9f290c3

• TST: update tutorials and "tests"

  xiaochendu

  committed
  5d6937f

• ENH: add additional argument to sample_pourbaix_surface.py

  Show description for 9452507
  xiaochendu

  committed
  9452507

• TST: update tests to follow new fix atoms Constraints

  xiaochendu

  committed
  55fb1ab

• BUG: update .gitignore to include missing test files and upload them

  xiaochendu

  committed
  fee856f

• Merge branch 'master' into refactoring

  xiaochendu

  committed
  0140f46

• MAINT: consolidate MCMC and SurfaceSystem arguments

  Show description for 19b5d97
  xiaochendu

  committed
  19b5d97

• TST: improve MCMC sampling tests

  Show description for 5467980
  xiaochendu

  committed
  5467980

• TST: remove GaN and Si "tests", update SrTiO3 tests to follow new SurfaceSystem signature

  xiaochendu

  committed
  659ae91

• MAINT: update gitignore to include .log and .csv files

  xiaochendu

  committed
  acf935b

• MAINT: move temperature setup, prepare_canonical to initialize(), renamed from set_up_mcmc_run()

  xiaochendu

  committed
  db91c2f

• MAINT: bring MCMC results outside of object and move plot to outside of main mcmc.py script

  Show description for 6f223af
  xiaochendu

  committed
  6f223af

Commits on Jun 29, 2024

• STY & BLD: update pre-commit-config and initial pyproject.toml

  xiaochendu

  committed
  c9de4be

• MAINT & DOC: refactored SurfaceSystem and revamped copy and todict + fromdict methods

  Show description for 48f8ba3
  xiaochendu

  committed
  48f8ba3

• TST & DOC: update tests and tutorial docs based on the previous commit

  xiaochendu

  committed
  4f85363

• TST & DOC: update tests and tutorial docs based on the previous commit

  xiaochendu

  committed
  6832170

• Merge branch 'refactoring' of github.mit.edu:MLMat/surface_sampling into refactoring

  xiaochendu

  committed
  9b0b3f1

• MAINT: remove saving and evaluating curr_energy in MCMC

  xiaochendu

  committed
  47be1c8

• TST & DOC: update tests and tutorials since self.relax is no longer provided to MCMC

  xiaochendu

  committed
  59b95c0

Commits on Jun 30, 2024

• ENH & MAINT & STY: implement get_logger

  Show description for 5534bef
  xiaochendu

  committed
  5534bef

• MAINT & DOC: renamed methods and moved functions/classes into more sensible locations

  Show description for 28596e2
  xiaochendu

  committed
  28596e2

Commits on Jul 1, 2024

• DEV: update gitignore

  xiaochendu

  committed
  99b0916

• DEV: update gitignore with more comprehensive list

  xiaochendu

  committed
  9da39c8

• MAINT: add class loggers for remainining Calculators

  xiaochendu

  committed
  842d822

• MAINT: make method signature clearer

  xiaochendu

  committed
  1d805f1

• ENH: make setup_logger clear existing loggers

  xiaochendu

  committed
  b48ace7

• ENH: generalize sample_surface_PaiNN.py to sample_surface.py

  Show description for 09d0e8c
  xiaochendu

  committed
  09d0e8c

Commits on Jul 2, 2024

• DEV: update gitignore with more comprehensive list

  xiaochendu

  committed
  7c8712a

• MAINT: rename mcmc.mcmc_run to mcmc.run

  xiaochendu

  committed
  d282be3

• ENH: add save statistics and more elegant update default settings to sample_surface.py

  xiaochendu

  committed
  42b695f

Commits on Jul 3, 2024

• ENH: add HydrogenPourbaixAtom to pourbaix atoms

  xiaochendu

  committed
  9273044

• Merge branch 'master' into pourbaix

  xiaochendu

  committed
  233d8b0

• Merge branch 'refactoring' into pourbaix

  xiaochendu

  committed
  6b0b408

• MAINT: update methods and classes with new generate_pourbaix_atoms signature

  xiaochendu

  committed
  4888445

• ENH: further integration of script helper/plotting functions into utils

  xiaochendu

  committed
  e5a0968

• MAINT: update clustering.py with code refactor

  xiaochendu

  committed
  2198f71

• ENH: add create_surface_formation_entries.py script

  Show description for aaa43c0
  xiaochendu

  committed
  aaa43c0

Commits on Jul 6, 2024

• MAINT: refactor data/resource paths and merge changes from pourbaix branch

  Show description for 58fea50
  xiaochendu

  committed
  58fea50

• MAINT & DOC: revamp scripts to follow new standard

  Show description for 41f1402
  xiaochendu

  committed
  41f1402

• BLD: Update dependencies and environment configuration

  Show description for d1eae4b
  xiaochendu

  committed
  d1eae4b

Commits on Jul 7, 2024

• BUG: recommit gitignored tutorials data files

  xiaochendu

  committed
  6fe5edf

• TST: update data path for test_filter_distance

  xiaochendu

  committed
  b4ac6f6

• MAINT: run tutorials notebooks (after commiting from offline)

  xiaochendu

  committed
  f74eb63

• MAINT & BUG: refactor util functions out of scripts and squash minor bugs

  xiaochendu

  committed
  b5ab922

• ENH: add tutorial to cut surfaces

  xiaochendu

  committed
  f61a389

• DOC: update README and add cover image

  xiaochendu

  committed
  eaeb59a

• BUG: minor bugs fixed

  Show description for cee8cbe
  xiaochendu

  committed
  cee8cbe

• BLD: update dependencies in pyproject.toml

  xiaochendu

  committed
  a161dcf

• DOC: update README.md for internal testing

  xiaochendu

  committed
  17080da

• MAINT & BUG: update latent space clustering script and tutorial

  Show description for 68a9ba0
  xiaochendu

  committed
  68a9ba0

• MAINT: remove legend for plot_dendrogram

  xiaochendu

  committed
  98396b3

Commits on Jul 8, 2024

• MAINT: remove sample_bulk.py for publishing

  xiaochendu

  committed
  784a3a6

• DOC: correction to README.md

  xiaochendu

  committed
  b6eb939

• MAINT: remove line from SrTiO3 tutorial

  xiaochendu

  committed
  ac73171

Commits on Jul 9, 2024

• MAINT: pass logger to helper functions in clustering.py

  xiaochendu

  committed
  cec57ad

• DOC: update tutorials and files

  xiaochendu

  committed
  1aa6119

• DOC: update latent space clustering in README with ensemble PaiNN NFF

  xiaochendu

  committed
  cef5786

• DOC: Add prepare_surface.ipynb to README

  xiaochendu

  committed
  b840097

Commits on Jul 10, 2024

• BLD: update environment files

  Show description for ae45bdd
  xiaochendu

  committed
  ae45bdd

• MAINT: fix docs and minor changes

  Show description for 677f6b5
  xiaochendu

  committed
  677f6b5

• MAINT: add correct LAMMPS potentials to repo and correct paths

  xiaochendu

  committed
  c30770f

Commits on Jul 18, 2024

• BUG: add colors.txt for plot_settings.py

  xiaochendu

  committed
  0ee0dda

• BLD: add scipy to dependency list

  xiaochendu

  committed
  ad50039

• MAINT: update README with correct badges and remove dev sections

  xiaochendu

  committed
  820ef89

• BLD: add nff to dependencies

  xiaochendu

  committed
  1d7c049

• MAINT: minor updates to tutorials

  xiaochendu

  committed
  cdb65fa